Citrus Sinensis ID: 025640

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250
Protein Sequence
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQPAAETS
Secondary Structure (PSIPRED)
ccccccccccccccccccHHHHHHHHHHHccccEEEEEcccEEEEEEEccccccccccccccccEEEEcccEEEEEEccHHcHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHcccccccccccEEEEEEEEEcccccEEEEEccccccccccEEEEcccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcccccccccEEEEEEEEEccccccEEEccHHHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHccccccEcccccEHHHHHHHHHHcccccEEEEEcccEEEEEEEcccccccEccccccccEEEccccEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHEcccccccEEEEEEEEEcccEEEEEEEcccccEEEEcEEEEcccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccccccHHHEEEEEEEEcccccEEEEEccHHHHHHHHHHHccccccHccc
Coil and Loop (DISEMBL)
msrrydsrttifspegrLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTststekmykidDHVACAVAGIMSDANILINTARVQAQRYTyayqepmpvEQLVQSLCDtkqgytqfgglrpfgvSFLFAgwdknygfqlymsdpsgnyggwkaaaIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKtmdstsltsdklELAEVflmpsgkvkyqvcspEALSKLLVKhgvtqpaaets
Flexible Loop (DISEMBL)
msrrydsrttifspegrLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTskllqtststekmykiDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVlsktmdstsltsdKLELAEVFLMPSGKVKYQVCSPEALSKLLVkhgvtqpaaets
Low Complexity Region (SEG)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKaaaigannqaaqSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQPAAETS
Disordered region (IsUnstruct)
**********IFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK**I***EAVQLALKVLS***********KLELAEVFLMPSGKVKYQVCSPEALSKLLVK***********
Disordered Region (DISOPRED)
****YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLV************
Disordered Region (DISEMBL)
********TTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK***********
Disordered Region (DISPRO)
****YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGV********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQPAAETS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	250	2.2.26 [Sep-21-2011]
O81148	250	Proteasome subunit alpha	yes	no	1.0	1.0	0.92	1e-136
P52427	250	Proteasome subunit alpha	N/A	no	1.0	1.0	0.912	1e-136
O82530	249	Proteasome subunit alpha	N/A	no	0.996	1.0	0.904	1e-132
Q5VRG3	250	Proteasome subunit alpha	yes	no	0.992	0.992	0.839	1e-124
P0C8Y9	250	Proteasome subunit alpha	N/A	no	0.992	0.992	0.839	1e-124
P0C1G8	250	Proteasome subunit alpha	yes	no	0.992	0.992	0.839	1e-124
A2Y9X7	250	Proteasome subunit alpha	N/A	no	0.992	0.992	0.839	1e-124
P34119	250	Proteasome subunit alpha	yes	no	0.972	0.972	0.638	1e-90
P23638	258	Proteasome subunit alpha	yes	no	0.972	0.941	0.602	1e-85
Q9R1P0	261	Proteasome subunit alpha	yes	no	0.944	0.904	0.600	9e-81

>sp|O81148|PSA4_ARATH Proteasome subunit alpha type-4 OS=Arabidopsis thaliana GN=PAC1 PE=1 SV=1

 Score =  484 bits (1247), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 230/250 (92%), Positives = 242/250 (96%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVL+GEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLIGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           S EKMYKIDDHVACAVAGIMSDANILINTARVQAQRYT+ YQEPMPVEQLVQSLCDTKQG
Sbjct: 61  SAEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTFMYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDK++GFQLYMSDPSGNYGGWKAAA+GANNQAAQSILKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKHHGFQLYMSDPSGNYGGWKAAAVGANNQAAQSILKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DD +REEAV+LALKVL+KTMDSTSLTS+KLELAEV+L PS  VKY V SPE+L+KLLVKH
Sbjct: 181 DDATREEAVELALKVLTKTMDSTSLTSEKLELAEVYLTPSKTVKYHVHSPESLTKLLVKH 240

Query: 241 GVTQPAAETS 250
           GVTQPAAETS
Sbjct: 241 GVTQPAAETS 250

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 4EC: .EC: 2EC: 5EC: .EC: 1

>sp|P52427|PSA4_SPIOL Proteasome subunit alpha type-4 OS=Spinacia oleracea GN=PAC1 PE=2 SV=1

 Score =  484 bits (1246), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 228/250 (91%), Positives = 245/250 (98%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGIL+KDGVVL+GEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILAKDGVVLIGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYT++YQEPMPVEQLVQSLCDTKQG
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTFSYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKA AIGANNQAAQS+LKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKATAIGANNQAAQSMLKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DD++RE+AV+LALK LSKTMDSTSLTS+KLELAEV+L+PSGKVKYQV SPE+L++LL + 
Sbjct: 181 DDVTREDAVKLALKALSKTMDSTSLTSEKLELAEVYLLPSGKVKYQVHSPESLNRLLTES 240

Query: 241 GVTQPAAETS 250
           G+TQPAAETS
Sbjct: 241 GLTQPAAETS 250

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Spinacia oleracea (taxid: 3562)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|O82530|PSA4_PETHY Proteasome subunit alpha type-4 OS=Petunia hybrida GN=PAC1 PE=2 SV=1

 Score =  471 bits (1212), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 226/250 (90%), Positives = 240/250 (96%), Gaps = 1/250 (0%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGI SKDGVVLVGEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGISSKDGVVLVGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           S+EKMYKIDDHVACAVAGIMSDANILINTARVQAQRYT++YQEPMPVEQLVQSLCDTKQG
Sbjct: 61  SSEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTFSYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQ+GGL PFGVSFLFAGWDKN+GFQL+MSDPSGNY GWKAAAIGANNQAAQS+LKQDYK
Sbjct: 121 YTQYGGLPPFGVSFLFAGWDKNFGFQLFMSDPSGNYAGWKAAAIGANNQAAQSMLKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DDI+REEAVQLALKVLSKTMDSTSLTS+KLELAEVFL  +GKVKYQ CSPE L+ +LVK 
Sbjct: 181 DDITREEAVQLALKVLSKTMDSTSLTSEKLELAEVFL-SNGKVKYQACSPEKLNSMLVKS 239

Query: 241 GVTQPAAETS 250
           G+TQP+AE S
Sbjct: 240 GLTQPSAEES 249

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Petunia hybrida (taxid: 4102)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q5VRG3|PSA4B_ORYSJ Proteasome subunit alpha type-4-2 OS=Oryza sativa subsp. japonica GN=Os06g0167600 PE=2 SV=1

 Score =  445 bits (1144), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 209/249 (83%), Positives = 233/249 (93%), Gaps = 1/249 (0%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSA+G+L+ DGVVLVGEKKVTSKLLQTS 
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSALGVLAADGVVLVGEKKVTSKLLQTSR 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           S EKMYKID H+ACAVAGIMSDANIL+NTAR+ AQRY  +YQEP+PVEQLVQSLCDTKQG
Sbjct: 61  SAEKMYKIDSHLACAVAGIMSDANILLNTARLHAQRYALSYQEPIPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDK++GFQLYMSDPSGNY GWKAAA+GAN+QAAQS+LKQDY+
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKHHGFQLYMSDPSGNYSGWKAAAVGANSQAAQSMLKQDYR 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP-SGKVKYQVCSPEALSKLLVK 239
           D ++REEAV LALKVLSKTMDSTSLT++KLELAEVFL P +G+V+YQVCSPEA+ KLL K
Sbjct: 181 DGLTREEAVALALKVLSKTMDSTSLTAEKLELAEVFLQPGTGEVQYQVCSPEAMGKLLAK 240

Query: 240 HGVTQPAAE 248
            G++QPA E
Sbjct: 241 AGLSQPAPE 249

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|P0C8Y9|PSA4B_ORYSI Proteasome subunit alpha type-4-2 OS=Oryza sativa subsp. indica GN=OsI_021067 PE=1 SV=1

 Score =  445 bits (1144), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 209/249 (83%), Positives = 233/249 (93%), Gaps = 1/249 (0%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSA+G+L+ DGVVLVGEKKVTSKLLQTS 
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSALGVLAADGVVLVGEKKVTSKLLQTSR 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           S EKMYKID H+ACAVAGIMSDANIL+NTAR+ AQRY  +YQEP+PVEQLVQSLCDTKQG
Sbjct: 61  SAEKMYKIDSHLACAVAGIMSDANILLNTARLHAQRYALSYQEPIPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDK++GFQLYMSDPSGNY GWKAAA+GAN+QAAQS+LKQDY+
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKHHGFQLYMSDPSGNYSGWKAAAVGANSQAAQSMLKQDYR 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP-SGKVKYQVCSPEALSKLLVK 239
           D ++REEAV LALKVLSKTMDSTSLT++KLELAEVFL P +G+V+YQVCSPEA+ KLL K
Sbjct: 181 DGLTREEAVALALKVLSKTMDSTSLTAEKLELAEVFLQPGTGEVQYQVCSPEAMGKLLAK 240

Query: 240 HGVTQPAAE 248
            G++QPA E
Sbjct: 241 AGLSQPAPE 249

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Oryza sativa subsp. indica (taxid: 39946)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|P0C1G8|PSA4A_ORYSJ Proteasome subunit alpha type-4-1 OS=Oryza sativa subsp. japonica GN=PAC1 PE=2 SV=1

 Score =  444 bits (1143), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 209/249 (83%), Positives = 233/249 (93%), Gaps = 1/249 (0%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSA+G+L+ DGVVLVGEKKVTSKLLQTS 
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSALGVLAADGVVLVGEKKVTSKLLQTSR 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           S EKMYKID H+ACAVAGIMSDANIL+NTAR+ AQRY  +YQEP+PVEQLVQSLCDTKQG
Sbjct: 61  SAEKMYKIDSHLACAVAGIMSDANILLNTARLHAQRYALSYQEPIPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDK++GFQLYMSDPSGNY GWKAAA+GAN+QAAQS+LKQDY+
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKHHGFQLYMSDPSGNYSGWKAAAVGANSQAAQSMLKQDYR 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP-SGKVKYQVCSPEALSKLLVK 239
           D ++REEAV LALKVLSKTMDSTSLT++KLELAEVFL P +G+V+YQVCSPEA+ KLL K
Sbjct: 181 DGMTREEAVALALKVLSKTMDSTSLTAEKLELAEVFLQPGTGEVQYQVCSPEAMGKLLAK 240

Query: 240 HGVTQPAAE 248
            G++QPA E
Sbjct: 241 AGLSQPAPE 249

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|A2Y9X7|PSA4A_ORYSI Proteasome subunit alpha type-4-1 OS=Oryza sativa subsp. indica GN=OsI_021120 PE=1 SV=2

 Score =  444 bits (1143), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 209/249 (83%), Positives = 233/249 (93%), Gaps = 1/249 (0%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSA+G+L+ DGVVLVGEKKVTSKLLQTS 
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSALGVLAADGVVLVGEKKVTSKLLQTSR 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           S EKMYKID H+ACAVAGIMSDANIL+NTAR+ AQRY  +YQEP+PVEQLVQSLCDTKQG
Sbjct: 61  SAEKMYKIDSHLACAVAGIMSDANILLNTARLHAQRYALSYQEPIPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDK++GFQLYMSDPSGNY GWKAAA+GAN+QAAQS+LKQDY+
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKHHGFQLYMSDPSGNYSGWKAAAVGANSQAAQSMLKQDYR 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP-SGKVKYQVCSPEALSKLLVK 239
           D ++REEAV LALKVLSKTMDSTSLT++KLELAEVFL P +G+V+YQVCSPEA+ KLL K
Sbjct: 181 DGMTREEAVALALKVLSKTMDSTSLTAEKLELAEVFLQPGTGEVQYQVCSPEAMGKLLAK 240

Query: 240 HGVTQPAAE 248
            G++QPA E
Sbjct: 241 AGLSQPAPE 249

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Oryza sativa subsp. indica (taxid: 39946)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|P34119|PSA4_DICDI Proteasome subunit alpha type-4 OS=Dictyostelium discoideum GN=psmA4 PE=2 SV=1

 Score =  332 bits (851), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 157/246 (63%), Positives = 196/246 (79%), Gaps = 3/246 (1%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           M+RRYD RTTIFSPEGR+YQVEYAM AI +AG+ +GIL+KDG+VL  EKK T+KLL +ST
Sbjct: 1   MARRYDQRTTIFSPEGRVYQVEYAMTAIRHAGATVGILAKDGIVLAAEKKTTAKLLDSST 60

Query: 61  S-TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQ 119
           S +EKM+KID+HV CAVAGI SDANILIN AR+ +QR+ Y YQEPMPVEQLV  +CDTKQ
Sbjct: 61  SISEKMFKIDEHVVCAVAGITSDANILINYARLSSQRFFYQYQEPMPVEQLVSQICDTKQ 120

Query: 120 GYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGA-NNQAAQSILKQD 178
           GYTQ+GGLRPFGVSFL+AGWD++YGFQLY SDPSGN+ GWKA +IG  N+Q AQS+L+ +
Sbjct: 121 GYTQYGGLRPFGVSFLYAGWDRHYGFQLYQSDPSGNFAGWKATSIGGENSQVAQSVLRSN 180

Query: 179 YKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLV 238
           YK DIS +EA+QLALKVL+KTMD +++ S+KLE +  F      V Y + +   L   + 
Sbjct: 181 YKPDISLKEALQLALKVLTKTMDRSNINSEKLEFS-YFTKQGDNVVYHIFTAAELDAFIK 239

Query: 239 KHGVTQ 244
           +  + Q
Sbjct: 240 ETDLEQ 245

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|P23638|PSA3_YEAST Proteasome subunit alpha type-3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PRE9 PE=1 SV=1

 Score =  316 bits (809), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 147/244 (60%), Positives = 193/244 (79%), Gaps = 1/244 (0%)

Query: 2   SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
           SRRYDSRTTIFSPEGRLYQVEYA+E+I +AG+AIGI++ DG+VL  E+KVTS LL+  TS
Sbjct: 3   SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 62

Query: 62  TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
           TEK+YK++D +A AVAG+ +DA ILINTAR+ AQ Y   Y E +PVE LV+ L D KQGY
Sbjct: 63  TEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGY 122

Query: 122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD 181
           TQ GGLRPFGVSF++AG+D  YG+QLY S+PSGNY GWKA ++GAN  AAQ++L+ DYKD
Sbjct: 123 TQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 182

Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPS-GKVKYQVCSPEALSKLLVKH 240
           D+  ++A++LALK LSKT DS++LT D+LE A +    + G+V  ++  P+ +  +LVK 
Sbjct: 183 DMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKT 242

Query: 241 GVTQ 244
           G+T+
Sbjct: 243 GITK 246

The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

>sp|Q9R1P0|PSA4_MOUSE Proteasome subunit alpha type-4 OS=Mus musculus GN=Psma4 PE=1 SV=1

 Score =  300 bits (767), Expect = 9e-81,   Method: Compositional matrix adjust.
 Identities = 143/238 (60%), Positives = 184/238 (77%), Gaps = 2/238 (0%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIG+AG+ +GIL+ DGV+L  E++   KLL    
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
            +EK+YK+++ +AC+VAGI SDAN+L N  R+ AQRY   YQEP+P EQLV +LCD KQ 
Sbjct: 61  FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGG RPFGVS L+ GWDK+YGFQLY SDPSGNYGGWKA  IG N+ AA S+LKQDYK
Sbjct: 121 YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK 180

Query: 181 D-DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
           + +++ + A+ LA+KVL+KTMD + L+++K+E+A      SGK   +V   + + +L+
Sbjct: 181 EGEMTLKSALALAVKVLNKTMDVSKLSAEKVEIA-TLTRESGKTVIRVLKQKEVEQLI 237

The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 5

EC: .

EC: 1

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	250
225462543	250	PREDICTED: proteasome subunit alpha type	1.0	1.0	0.964	1e-139
356568146	250	PREDICTED: proteasome subunit alpha type	1.0	1.0	0.956	1e-139
449456526	250	PREDICTED: proteasome subunit alpha type	1.0	1.0	0.952	1e-138
356496249	250	PREDICTED: proteasome subunit alpha type	1.0	1.0	0.948	1e-138
255540109	250	proteasome subunit alpha type, putative	1.0	1.0	0.94	1e-138
357482775	250	Proteasome subunit alpha type [Medicago	1.0	1.0	0.944	1e-138
388491474	250	unknown [Medicago truncatula] gi|3885179	1.0	1.0	0.94	1e-138
224086367	250	predicted protein [Populus trichocarpa]	1.0	1.0	0.948	1e-138
356521060	250	PREDICTED: proteasome subunit alpha type	1.0	1.0	0.944	1e-137
255540107	250	proteasome subunit alpha type, putative	1.0	1.0	0.94	1e-137

>gi|225462543|ref|XP_002266917.1| PREDICTED: proteasome subunit alpha type-4 isoform 2 [Vitis vinifera] gi|225462545|ref|XP_002266877.1| PREDICTED: proteasome subunit alpha type-4 isoform 1 [Vitis vinifera] gi|147799989|emb|CAN77245.1| hypothetical protein VITISV_018657 [Vitis vinifera]

 Score =  499 bits (1284), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 241/250 (96%), Positives = 246/250 (98%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAG+AIGILSKDGVVLVGEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDKN+GFQLYMSDPSGNYGGWKAAAIGANNQAAQS+LKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNFGFQLYMSDPSGNYGGWKAAAIGANNQAAQSMLKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DDISRE+AVQLALKVLSKTMDSTSLTSDKLELAEVFL  SGKVKYQVCS +ALSKLLVK 
Sbjct: 181 DDISREDAVQLALKVLSKTMDSTSLTSDKLELAEVFLSASGKVKYQVCSADALSKLLVKF 240

Query: 241 GVTQPAAETS 250
           GVTQPAAETS
Sbjct: 241 GVTQPAAETS 250

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356568146|ref|XP_003552274.1| PREDICTED: proteasome subunit alpha type-4-like isoform 1 [Glycine max]

 Score =  498 bits (1283), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 239/250 (95%), Positives = 246/250 (98%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAG+AIGILSKDGVVLVGEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDKN+GFQLY SDPSGNYGGWKAAAIGANNQAAQSILKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNFGFQLYTSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DDI+REEAVQLALKVLSKTMDSTSLTS+KLELAEVFL PSGKVKYQVCSPE L+KLLVK 
Sbjct: 181 DDITREEAVQLALKVLSKTMDSTSLTSEKLELAEVFLSPSGKVKYQVCSPENLTKLLVKF 240

Query: 241 GVTQPAAETS 250
           GVTQPAA+T+
Sbjct: 241 GVTQPAADTA 250

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449456526|ref|XP_004146000.1| PREDICTED: proteasome subunit alpha type-4-like [Cucumis sativus] gi|449518445|ref|XP_004166252.1| PREDICTED: proteasome subunit alpha type-4-like isoform 1 [Cucumis sativus] gi|449518447|ref|XP_004166253.1| PREDICTED: proteasome subunit alpha type-4-like isoform 2 [Cucumis sativus]

 Score =  497 bits (1280), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 238/250 (95%), Positives = 245/250 (98%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           STEKMYK+DDHVACAVAGIMSDANILINTARVQA RYTYAYQEPMPVEQLVQSLCDTKQG
Sbjct: 61  STEKMYKLDDHVACAVAGIMSDANILINTARVQAMRYTYAYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQS+LKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSMLKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DDISREEA+QLALKVLSKTMDSTSLTS+KLELAEVFL PSG VKYQVCSPE++SKLLVK 
Sbjct: 181 DDISREEAIQLALKVLSKTMDSTSLTSEKLELAEVFLSPSGSVKYQVCSPESVSKLLVKS 240

Query: 241 GVTQPAAETS 250
           G+TQPAAE S
Sbjct: 241 GLTQPAAEAS 250

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496249|ref|XP_003516981.1| PREDICTED: proteasome subunit alpha type-4-like isoform 1 [Glycine max] gi|356496251|ref|XP_003516982.1| PREDICTED: proteasome subunit alpha type-4-like isoform 2 [Glycine max]

 Score =  497 bits (1280), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 237/250 (94%), Positives = 246/250 (98%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAG+AIGILSKDGVVLVGEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDKN+GFQLYMSDPSGNYGGWKA AIGANNQAAQSILKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNFGFQLYMSDPSGNYGGWKAGAIGANNQAAQSILKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DDI+REEAVQLALKVLSKTMDSTSLTS+KLELAEVFL PSGKVKY+VCSPEAL+K+LVK 
Sbjct: 181 DDITREEAVQLALKVLSKTMDSTSLTSEKLELAEVFLSPSGKVKYEVCSPEALTKMLVKS 240

Query: 241 GVTQPAAETS 250
           GVTQPA +T+
Sbjct: 241 GVTQPATDTA 250

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540109|ref|XP_002511119.1| proteasome subunit alpha type, putative [Ricinus communis] gi|223550234|gb|EEF51721.1| proteasome subunit alpha type, putative [Ricinus communis]

 Score =  496 bits (1277), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 235/250 (94%), Positives = 247/250 (98%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAG+AIGILSKDG VLVGEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGAVLVGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDKN+GFQLYMSDPSGNYGGWKAAA+GANNQAAQS+LKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNFGFQLYMSDPSGNYGGWKAAAVGANNQAAQSMLKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DDI+REEAVQLALKVLSKTMDSTSLTSDKLELAEVFL+PSG+VKYQVCSP++LSKLLVK 
Sbjct: 181 DDITREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLLPSGEVKYQVCSPDSLSKLLVKS 240

Query: 241 GVTQPAAETS 250
           G+TQP+A+ S
Sbjct: 241 GMTQPSADAS 250

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357482775|ref|XP_003611674.1| Proteasome subunit alpha type [Medicago truncatula] gi|355513009|gb|AES94632.1| Proteasome subunit alpha type [Medicago truncatula]

 Score =  496 bits (1276), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 236/250 (94%), Positives = 244/250 (97%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAG+AIGILSKDGVVLVGEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           STEKMYKIDDHVACAVAGIMSDANILINTAR+QAQRY++AYQEPMPVEQLVQSLCDTKQG
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARIQAQRYSFAYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDKN+GFQLYMSDPSGNYGGWKA AIGANNQAAQSILKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNFGFQLYMSDPSGNYGGWKAGAIGANNQAAQSILKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DDI+REEAV LALKVLSKTMDSTSLTSDKLELAEVFL PSGKVKYQVCSPE L+KLLVK 
Sbjct: 181 DDITREEAVNLALKVLSKTMDSTSLTSDKLELAEVFLAPSGKVKYQVCSPENLTKLLVKS 240

Query: 241 GVTQPAAETS 250
           GVTQPA ET+
Sbjct: 241 GVTQPATETA 250

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388491474|gb|AFK33803.1| unknown [Medicago truncatula] gi|388517995|gb|AFK47059.1| unknown [Medicago truncatula]

 Score =  495 bits (1275), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 235/250 (94%), Positives = 246/250 (98%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAG+AIGILSKDGVVLVGEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           STEKMYKIDDHVACAVAGIMSDANILINTAR+QAQRY++AYQEPMPVEQLVQSLCDTKQG
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARIQAQRYSFAYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDKN+GFQLYMSDPSGNYGGWKA+AIGANNQAAQSILKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNFGFQLYMSDPSGNYGGWKASAIGANNQAAQSILKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DDI+REEAVQLALKVLSKTMDSTSLTS+KLELAEVFL PSGKVKYQVCSPE L+KLLVK 
Sbjct: 181 DDITREEAVQLALKVLSKTMDSTSLTSEKLELAEVFLSPSGKVKYQVCSPENLTKLLVKS 240

Query: 241 GVTQPAAETS 250
           GVTQPA +T+
Sbjct: 241 GVTQPATDTA 250

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224086367|ref|XP_002307867.1| predicted protein [Populus trichocarpa] gi|118484506|gb|ABK94128.1| unknown [Populus trichocarpa] gi|222853843|gb|EEE91390.1| predicted protein [Populus trichocarpa]

 Score =  495 bits (1274), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 237/250 (94%), Positives = 244/250 (97%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           STEKMYKIDDHVACAVAGIMSDANILINTAR+QAQRYT+AYQEPMPVEQLVQSLCDTKQG
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARIQAQRYTFAYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNY GWKA AIGANNQAAQS+LKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYSGWKAGAIGANNQAAQSMLKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           D+I+REEAVQLALKVLSKTMDSTSLTS+KLELAEVFL PSG VKYQVCSP+ LSKLLVK 
Sbjct: 181 DEITREEAVQLALKVLSKTMDSTSLTSEKLELAEVFLSPSGNVKYQVCSPDVLSKLLVKF 240

Query: 241 GVTQPAAETS 250
           GVTQPAAETS
Sbjct: 241 GVTQPAAETS 250

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521060|ref|XP_003529176.1| PREDICTED: proteasome subunit alpha type-4-like isoform 1 [Glycine max] gi|356521062|ref|XP_003529177.1| PREDICTED: proteasome subunit alpha type-4-like isoform 2 [Glycine max]

 Score =  494 bits (1271), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 236/250 (94%), Positives = 244/250 (97%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAG+AIGILSKDGVVLVGEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGVVLVGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRY YAYQEPMPVEQLVQSLCDTKQG
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYAYAYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDKN+GFQLY SDPSGNYGGWKAAAIGANNQAAQSILKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNFGFQLYTSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DDI+REEAVQLALKVLSKTMDSTSLTS+KLELAEVFL P+GKVKYQVCSPE L+KLLVK 
Sbjct: 181 DDITREEAVQLALKVLSKTMDSTSLTSEKLELAEVFLSPAGKVKYQVCSPENLTKLLVKF 240

Query: 241 GVTQPAAETS 250
           GVTQPA +T+
Sbjct: 241 GVTQPATDTA 250

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540107|ref|XP_002511118.1| proteasome subunit alpha type, putative [Ricinus communis] gi|223550233|gb|EEF51720.1| proteasome subunit alpha type, putative [Ricinus communis]

 Score =  493 bits (1269), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 235/250 (94%), Positives = 246/250 (98%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAG+AIGILSKDG VLVGEKKVTSKLLQTST
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGTAIGILSKDGAVLVGEKKVTSKLLQTST 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           STEKMYKIDDHVACAVAGIMSDANILINTARVQAQ YTYAYQEPMPVEQLVQSLCDTKQG
Sbjct: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQCYTYAYQEPMPVEQLVQSLCDTKQG 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAGWDKN+GFQLYMSDPSGNYGGWKAAA+GANNQAAQS+LKQDYK
Sbjct: 121 YTQFGGLRPFGVSFLFAGWDKNFGFQLYMSDPSGNYGGWKAAAVGANNQAAQSMLKQDYK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           DDI+REEAVQLALKVLSKTMDSTSLTSDKLELAEVFL+PSG+VKYQVCSP++LSKLLVK 
Sbjct: 181 DDITREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLLPSGEVKYQVCSPDSLSKLLVKS 240

Query: 241 GVTQPAAETS 250
           GVTQP+A+ S
Sbjct: 241 GVTQPSADAS 250

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	250
TAIR|locus:2090399	250	PAC1 "20S proteasome alpha sub	1.0	1.0	0.876	1.9e-113
DICTYBASE|DDB_G0280969	250	psmA4 "proteasome subunit alph	0.972	0.972	0.609	3.4e-77
ASPGD|ASPL0000051129	255	ssfA [Emericella nidulans (tax	0.976	0.956	0.602	8.1e-76
SGD|S000003367	258	PRE9 "Alpha 3 subunit of the 2	0.972	0.941	0.573	9.6e-73
CGD|CAL0004819	251	PRE9 [Candida albicans (taxid:	0.968	0.964	0.578	5.3e-72
UNIPROTKB|Q5AEB8	251	PRE9 "Putative uncharacterized	0.968	0.964	0.578	5.3e-72
ZFIN|ZDB-GENE-040426-1932	261	psma4 "proteasome (prosome, ma	0.988	0.946	0.566	6.7e-72
MGI|MGI:1347060	261	Psma4 "proteasome (prosome, ma	0.988	0.946	0.566	1.8e-71
UNIPROTKB|Q3ZCK9	261	PSMA4 "Proteasome subunit alph	0.988	0.946	0.562	2.9e-71
UNIPROTKB|P25789	261	PSMA4 "Proteasome subunit alph	0.988	0.946	0.562	2.9e-71

TAIR|locus:2090399 PAC1 "20S proteasome alpha subunit C1" [Arabidopsis thaliana (taxid:3702)]

 Score = 1119 (399.0 bits), Expect = 1.9e-113, P = 1.9e-113
 Identities = 219/250 (87%), Positives = 230/250 (92%)

Query:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
             MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVL+GEKKVTSKLLQTST
Sbjct:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLIGEKKVTSKLLQTST 60

Query:    61 STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
             S EKMYKIDDHVACAVAGIMSDANILINTARVQAQRYT+ YQEPMPVEQLVQSLCDTKQG
Sbjct:    61 SAEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTFMYQEPMPVEQLVQSLCDTKQG 120

Query:   121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK 180
             YTQFGGLRPFGVSFLFAGWDK++GFQLYMSDPSGNYGGWK            SILKQDYK
Sbjct:   121 YTQFGGLRPFGVSFLFAGWDKHHGFQLYMSDPSGNYGGWKAAAVGANNQAAQSILKQDYK 180

Query:   181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
             DD +REEAV+LALKVL+KTMDSTSLTS+KLELAEV+L PS  VKY V SPE+L+KLLVKH
Sbjct:   181 DDATREEAVELALKVLTKTMDSTSLTSEKLELAEVYLTPSKTVKYHVHSPESLTKLLVKH 240

Query:   241 GVTQPAAETS 250
             GVTQPAAETS
Sbjct:   241 GVTQPAAETS 250

GO:0004175 "endopeptidase activity" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0005839 "proteasome core complex" evidence=IEA;TAS

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA;TAS

GO:0008233 "peptidase activity" evidence=ISS

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=IEA

GO:0005773 "vacuole" evidence=IDA

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0046686 "response to cadmium ion" evidence=IEP;RCA

GO:0000502 "proteasome complex" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006094 "gluconeogenesis" evidence=RCA

GO:0006096 "glycolysis" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

DICTYBASE|DDB_G0280969 psmA4 "proteasome subunit alpha type 4" [Dictyostelium discoideum (taxid:44689)]

 Score = 777 (278.6 bits), Expect = 3.4e-77, P = 3.4e-77
 Identities = 150/246 (60%), Positives = 187/246 (76%)

Query:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
             M+RRYD RTTIFSPEGR+YQVEYAM AI +AG+ +GIL+KDG+VL  EKK T+KLL +ST
Sbjct:     1 MARRYDQRTTIFSPEGRVYQVEYAMTAIRHAGATVGILAKDGIVLAAEKKTTAKLLDSST 60

Query:    61 S-TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQ 119
             S +EKM+KID+HV CAVAGI SDANILIN AR+ +QR+ Y YQEPMPVEQLV  +CDTKQ
Sbjct:    61 SISEKMFKIDEHVVCAVAGITSDANILINYARLSSQRFFYQYQEPMPVEQLVSQICDTKQ 120

Query:   120 GYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXX-SILKQD 178
             GYTQ+GGLRPFGVSFL+AGWD++YGFQLY SDPSGN+ GWK             S+L+ +
Sbjct:   121 GYTQYGGLRPFGVSFLYAGWDRHYGFQLYQSDPSGNFAGWKATSIGGENSQVAQSVLRSN 180

Query:   179 YKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLV 238
             YK DIS +EA+QLALKVL+KTMD +++ S+KLE +  F      V Y + +   L   + 
Sbjct:   181 YKPDISLKEALQLALKVLTKTMDRSNINSEKLEFS-YFTKQGDNVVYHIFTAAELDAFIK 239

Query:   239 KHGVTQ 244
             +  + Q
Sbjct:   240 ETDLEQ 245

GO:0008233 "peptidase activity" evidence=IEA;IDA

GO:0006508 "proteolysis" evidence=IEA;IDA

GO:0005737 "cytoplasm" evidence=IEA;IPI

GO:0005634 "nucleus" evidence=IEA;IPI

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=IEA

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0005839 "proteasome core complex" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0004175 "endopeptidase activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

ASPGD|ASPL0000051129 ssfA [Emericella nidulans (taxid:162425)]

 Score = 764 (274.0 bits), Expect = 8.1e-76, P = 8.1e-76
 Identities = 147/244 (60%), Positives = 185/244 (75%)

Query:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
             MSRRYDSRTTIFSPEGRLYQVEYA+EAI +AG+A+GIL+KDG+VL  EKKVTSKLL+  T
Sbjct:     1 MSRRYDSRTTIFSPEGRLYQVEYALEAISHAGTALGILAKDGIVLAAEKKVTSKLLEQDT 60

Query:    61 STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
             S EK+Y ++D++ CAVAG+ +DANILIN AR  AQRY   Y E +P EQLV+ LCD KQG
Sbjct:    61 SAEKLYTLNDNMICAVAGMTADANILINYARQAAQRYLITYGEEIPCEQLVRRLCDLKQG 120

Query:   121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK 180
             YTQ GGLRPFGVSF++AG+D    FQLY S+PSGNYGGWK            S+LKQDYK
Sbjct:   121 YTQHGGLRPFGVSFIYAGYDHLREFQLYQSNPSGNYGGWKATSVGANNASAQSLLKQDYK 180

Query:   181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
             +D   +EA  +A+KVLSKTMDST L+S+K+E A V     GK+ + + + + ++ LL +H
Sbjct:   181 EDCDLKEACAMAVKVLSKTMDSTKLSSEKIEFATVGKTKEGKIYHHLWNADEINALLKEH 240

Query:   241 GVTQ 244
             G+ +
Sbjct:   241 GLAK 244

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA;ISA

GO:0030010 "establishment of cell polarity" evidence=IGI

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0034515 "proteasome storage granule" evidence=IEA

GO:0080129 "proteasome core complex assembly" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0010499 "proteasomal ubiquitin-independent protein catabolic process" evidence=IEA

SGD|S000003367 PRE9 "Alpha 3 subunit of the 20S proteasome" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 735 (263.8 bits), Expect = 9.6e-73, P = 9.6e-73
 Identities = 140/244 (57%), Positives = 184/244 (75%)

Query:     2 SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
             SRRYDSRTTIFSPEGRLYQVEYA+E+I +AG+AIGI++ DG+VL  E+KVTS LL+  TS
Sbjct:     3 SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 62

Query:    62 TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
             TEK+YK++D +A AVAG+ +DA ILINTAR+ AQ Y   Y E +PVE LV+ L D KQGY
Sbjct:    63 TEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGY 122

Query:   122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKD 181
             TQ GGLRPFGVSF++AG+D  YG+QLY S+PSGNY GWK            ++L+ DYKD
Sbjct:   123 TQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 182

Query:   182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPS-GKVKYQVCSPEALSKLLVKH 240
             D+  ++A++LALK LSKT DS++LT D+LE A +    + G+V  ++  P+ +  +LVK 
Sbjct:   183 DMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKT 242

Query:   241 GVTQ 244
             G+T+
Sbjct:   243 GITK 246

GO:0010499 "proteasomal ubiquitin-independent protein catabolic process" evidence=IDA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0005839 "proteasome core complex" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA;IDA

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IDA

GO:0000502 "proteasome complex" evidence=IEA

GO:0034515 "proteasome storage granule" evidence=IDA

GO:0005634 "nucleus" evidence=IEA;IC

GO:0005737 "cytoplasm" evidence=IEA

GO:0042175 "nuclear outer membrane-endoplasmic reticulum membrane network" evidence=IC

GO:0080129 "proteasome core complex assembly" evidence=IMP

GO:0003674 "molecular_function" evidence=ND

GO:0006508 "proteolysis" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

GO:0004175 "endopeptidase activity" evidence=IEA

CGD|CAL0004819 PRE9 [Candida albicans (taxid:5476)]

 Score = 728 (261.3 bits), Expect = 5.3e-72, P = 5.3e-72
 Identities = 140/242 (57%), Positives = 180/242 (74%)

Query:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
             MSRRYDSRTTIFSPEGRLYQVEYA EAI NAG+AIGILS +GVVL  EKKVTSKLL    
Sbjct:     1 MSRRYDSRTTIFSPEGRLYQVEYAQEAISNAGTAIGILSPEGVVLACEKKVTSKLLDDDG 60

Query:    61 STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
             S EK+Y I+D + CAVAG+ +DA+IL+N AR+QAQ+Y   Y E +P E L+  +CD KQG
Sbjct:    61 SAEKLYIINDQMICAVAGMTADASILVNNARIQAQQYLKLYDEEIPCEMLINRVCDVKQG 120

Query:   121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK 180
             YTQ GGLRPFGVSFL+AG+D  Y FQL+ S+PSGNY GWK            ++LK+DYK
Sbjct:   121 YTQHGGLRPFGVSFLYAGYDDRYQFQLFTSNPSGNYSGWKATSIGANNSAAQTLLKKDYK 180

Query:   181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
             DD++ ++A +LA+KVLSKTMD++++ S+KLE A + L    KV +++ + + +  L+   
Sbjct:   181 DDLTLKDACELAIKVLSKTMDASNINSEKLEFATLSLGKDNKVLHKIWNDKDIDILIKAS 240

Query:   241 GV 242
             GV
Sbjct:   241 GV 242

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=ISS

GO:0005839 "proteasome core complex" evidence=IDA

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0034515 "proteasome storage granule" evidence=IEA

GO:0080129 "proteasome core complex assembly" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0010499 "proteasomal ubiquitin-independent protein catabolic process" evidence=IEA

UNIPROTKB|Q5AEB8 PRE9 "Putative uncharacterized protein PRE9" [Candida albicans SC5314 (taxid:237561)]

 Score = 728 (261.3 bits), Expect = 5.3e-72, P = 5.3e-72
 Identities = 140/242 (57%), Positives = 180/242 (74%)

Query:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
             MSRRYDSRTTIFSPEGRLYQVEYA EAI NAG+AIGILS +GVVL  EKKVTSKLL    
Sbjct:     1 MSRRYDSRTTIFSPEGRLYQVEYAQEAISNAGTAIGILSPEGVVLACEKKVTSKLLDDDG 60

Query:    61 STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
             S EK+Y I+D + CAVAG+ +DA+IL+N AR+QAQ+Y   Y E +P E L+  +CD KQG
Sbjct:    61 SAEKLYIINDQMICAVAGMTADASILVNNARIQAQQYLKLYDEEIPCEMLINRVCDVKQG 120

Query:   121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK 180
             YTQ GGLRPFGVSFL+AG+D  Y FQL+ S+PSGNY GWK            ++LK+DYK
Sbjct:   121 YTQHGGLRPFGVSFLYAGYDDRYQFQLFTSNPSGNYSGWKATSIGANNSAAQTLLKKDYK 180

Query:   181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
             DD++ ++A +LA+KVLSKTMD++++ S+KLE A + L    KV +++ + + +  L+   
Sbjct:   181 DDLTLKDACELAIKVLSKTMDASNINSEKLEFATLSLGKDNKVLHKIWNDKDIDILIKAS 240

Query:   241 GV 242
             GV
Sbjct:   241 GV 242

GO:0005839 "proteasome core complex" evidence=IDA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=ISS

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=ISS

ZFIN|ZDB-GENE-040426-1932 psma4 "proteasome (prosome, macropain) subunit, alpha type, 4" [Danio rerio (taxid:7955)]

 Score = 727 (261.0 bits), Expect = 6.7e-72, P = 6.7e-72
 Identities = 141/249 (56%), Positives = 183/249 (73%)

Query:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
             MSRRYDSRTTIFSPEGRLYQVEYAMEAIG+AG+ +GIL+ DGV+L  E++   KLL    
Sbjct:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60

Query:    61 STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
              +EK+YK+++ +AC+VAGI SDAN+L N  R+ AQRY   YQEP+P EQLV +LCD KQ 
Sbjct:    61 FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA 120

Query:   121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK 180
             YTQFGG RPFGVS L+ GWDK+YGFQLY SDPSGNYGGWK            S+LKQDYK
Sbjct:   121 YTQFGGKRPFGVSLLYMGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK 180

Query:   181 D-DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
             + +++   A+ LA+KVL+KTMD + L+++K+E+A +    +GK K +V   + + +L+ K
Sbjct:   181 EGEMTLSAALALAVKVLNKTMDVSKLSAEKVEIATL-TRENGKTKIKVLKQKEVEELIKK 239

Query:   240 HGVTQPAAE 248
             H   +  AE
Sbjct:   240 HEAEEAKAE 248

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=IEA

GO:0004175 "endopeptidase activity" evidence=IEA

GO:0005839 "proteasome core complex" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0006508 "proteolysis" evidence=IEA

MGI|MGI:1347060 Psma4 "proteasome (prosome, macropain) subunit, alpha type 4" [Mus musculus (taxid:10090)]

 Score = 723 (259.6 bits), Expect = 1.8e-71, P = 1.8e-71
 Identities = 141/249 (56%), Positives = 183/249 (73%)

Query:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
             MSRRYDSRTTIFSPEGRLYQVEYAMEAIG+AG+ +GIL+ DGV+L  E++   KLL    
Sbjct:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60

Query:    61 STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
              +EK+YK+++ +AC+VAGI SDAN+L N  R+ AQRY   YQEP+P EQLV +LCD KQ 
Sbjct:    61 FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA 120

Query:   121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK 180
             YTQFGG RPFGVS L+ GWDK+YGFQLY SDPSGNYGGWK            S+LKQDYK
Sbjct:   121 YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK 180

Query:   181 D-DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
             + +++ + A+ LA+KVL+KTMD + L+++K+E+A +    SGK   +V   + + +L+ K
Sbjct:   181 EGEMTLKSALALAVKVLNKTMDVSKLSAEKVEIATL-TRESGKTVIRVLKQKEVEQLIKK 239

Query:   240 HGVTQPAAE 248
             H   +  AE
Sbjct:   240 HEEEEAKAE 248

GO:0000502 "proteasome complex" evidence=IEA

GO:0004175 "endopeptidase activity" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005839 "proteasome core complex" evidence=IDA

GO:0006508 "proteolysis" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

GO:0051603 "proteolysis involved in cellular protein catabolic process" evidence=IEA

UNIPROTKB|Q3ZCK9 PSMA4 "Proteasome subunit alpha type-4" [Bos taurus (taxid:9913)]

 Score = 721 (258.9 bits), Expect = 2.9e-71, P = 2.9e-71
 Identities = 140/249 (56%), Positives = 183/249 (73%)

Query:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
             MSRRYDSRTTIFSPEGRLYQVEYAMEAIG+AG+ +GIL+ DGV+L  E++   KLL    
Sbjct:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60

Query:    61 STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
              +EK+YK+++ +AC+VAGI SDAN+L N  R+ AQRY   YQEP+P EQLV +LCD KQ 
Sbjct:    61 FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA 120

Query:   121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK 180
             YTQFGG RPFGVS L+ GWDK+YGFQLY SDPSGNYGGWK            S+LKQDYK
Sbjct:   121 YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK 180

Query:   181 D-DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
             + +++ + A+ LA+KVL+KTMD + L+++K+E+A +    +GK   +V   + + +L+ K
Sbjct:   181 EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATL-TRENGKTVIRVLKQKEVEQLIKK 239

Query:   240 HGVTQPAAE 248
             H   +  AE
Sbjct:   240 HEEEEAKAE 248

GO:0000932 "cytoplasmic mRNA processing body" evidence=ISS

GO:0005839 "proteasome core complex" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

UNIPROTKB|P25789 PSMA4 "Proteasome subunit alpha type-4" [Homo sapiens (taxid:9606)]

 Score = 721 (258.9 bits), Expect = 2.9e-71, P = 2.9e-71
 Identities = 140/249 (56%), Positives = 183/249 (73%)

Query:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
             MSRRYDSRTTIFSPEGRLYQVEYAMEAIG+AG+ +GIL+ DGV+L  E++   KLL    
Sbjct:     1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60

Query:    61 STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
              +EK+YK+++ +AC+VAGI SDAN+L N  R+ AQRY   YQEP+P EQLV +LCD KQ 
Sbjct:    61 FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA 120

Query:   121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK 180
             YTQFGG RPFGVS L+ GWDK+YGFQLY SDPSGNYGGWK            S+LKQDYK
Sbjct:   121 YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK 180

Query:   181 D-DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
             + +++ + A+ LA+KVL+KTMD + L+++K+E+A +    +GK   +V   + + +L+ K
Sbjct:   181 EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATL-TRENGKTVIRVLKQKEVEQLIKK 239

Query:   240 HGVTQPAAE 248
             H   +  AE
Sbjct:   240 HEEEEAKAE 248

GO:0019773 "proteasome core complex, alpha-subunit complex" evidence=IEA

GO:0004298 "threonine-type endopeptidase activity" evidence=IEA

GO:0019048 "virus-host interaction" evidence=IEA

GO:0000932 "cytoplasmic mRNA processing body" evidence=ISS

GO:0005839 "proteasome core complex" evidence=ISS

GO:0000502 "proteasome complex" evidence=TAS

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000209 "protein polyubiquitination" evidence=TAS

GO:0000216 "M/G1 transition of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0002474 "antigen processing and presentation of peptide antigen via MHC class I" evidence=TAS

GO:0002479 "antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006521 "regulation of cellular amino acid metabolic process" evidence=TAS

GO:0006915 "apoptotic process" evidence=TAS

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0031145 "anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" evidence=TAS

GO:0034641 "cellular nitrogen compound metabolic process" evidence=TAS

GO:0042590 "antigen processing and presentation of exogenous peptide antigen via MHC class I" evidence=TAS

GO:0042981 "regulation of apoptotic process" evidence=TAS

GO:0044281 "small molecule metabolic process" evidence=TAS

GO:0051436 "negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051437 "positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051439 "regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
C3NHC6	PSA_SULIN	3, ., 4, ., 2, 5, ., 1	0.4593	0.824	0.8547	yes	no
A6VIP0	PSA_METM7	3, ., 4, ., 2, 5, ., 1	0.4317	0.884	0.8532	yes	no
Q9UXC6	PSA_SULSO	3, ., 4, ., 2, 5, ., 1	0.4545	0.824	0.8547	yes	no
O59219	PSA_PYRHO	3, ., 4, ., 2, 5, ., 1	0.4463	0.9	0.8653	yes	no
A4FZT6	PSA_METM5	3, ., 4, ., 2, 5, ., 1	0.4361	0.884	0.8532	yes	no
Q4R932	PSA4_MACFA	3, ., 4, ., 2, 5, ., 1	0.5924	0.944	0.9042	N/A	no
P18053	PSA4_DROME	3, ., 4, ., 2, 5, ., 1	0.5491	0.956	0.9053	yes	no
C3MVG1	PSA_SULIM	3, ., 4, ., 2, 5, ., 1	0.4593	0.824	0.8547	yes	no
C4KHD9	PSA_SULIK	3, ., 4, ., 2, 5, ., 1	0.4593	0.824	0.8547	yes	no
Q9N599	PSA4_CAEEL	3, ., 4, ., 2, 5, ., 1	0.6338	0.844	0.844	yes	no
Q9YC01	PSA_AERPE	3, ., 4, ., 2, 5, ., 1	0.4292	0.84	0.8139	yes	no
Q5VRG3	PSA4B_ORYSJ	3, ., 4, ., 2, 5, ., 1	0.8393	0.992	0.992	yes	no
P23638	PSA3_YEAST	3, ., 4, ., 2, 5, ., 1	0.6024	0.972	0.9418	yes	no
P25789	PSA4_HUMAN	3, ., 4, ., 2, 5, ., 1	0.5966	0.944	0.9042	yes	no
Q09682	PSA3_SCHPO	3, ., 4, ., 2, 5, ., 1	0.5755	0.976	0.9838	yes	no
Q469M6	PSA_METBF	3, ., 4, ., 2, 5, ., 1	0.3893	0.936	0.9397	yes	no
Q9V122	PSA_PYRAB	3, ., 4, ., 2, 5, ., 1	0.4420	0.9	0.8653	yes	no
A9A846	PSA_METM6	3, ., 4, ., 2, 5, ., 1	0.4273	0.884	0.8532	yes	no
C3NEC6	PSA_SULIY	3, ., 4, ., 2, 5, ., 1	0.4593	0.824	0.8547	yes	no
A2Y9X7	PSA4A_ORYSI	3, ., 4, ., 2, 5, ., 1	0.8393	0.992	0.992	N/A	no
Q9R1P0	PSA4_MOUSE	3, ., 4, ., 2, 5, ., 1	0.6008	0.944	0.9042	yes	no
P52427	PSA4_SPIOL	3, ., 4, ., 2, 5, ., 1	0.912	1.0	1.0	N/A	no
Q8TYB7	PSA_METKA	3, ., 4, ., 2, 5, ., 1	0.4597	0.832	0.8455	yes	no
O29760	PSA_ARCFU	3, ., 4, ., 2, 5, ., 1	0.4502	0.828	0.8414	yes	no
C3MQ43	PSA_SULIL	3, ., 4, ., 2, 5, ., 1	0.4593	0.824	0.8547	yes	no
O81148	PSA4_ARATH	3, ., 4, ., 2, 5, ., 1	0.92	1.0	1.0	yes	no
P34119	PSA4_DICDI	3, ., 4, ., 2, 5, ., 1	0.6382	0.972	0.972	yes	no
P21670	PSA4_RAT	3, ., 4, ., 2, 5, ., 1	0.5966	0.944	0.9042	yes	no
C6A459	PSA_THESM	3, ., 4, ., 2, 5, ., 1	0.4506	0.9	0.8653	yes	no
P0C8Y9	PSA4B_ORYSI	3, ., 4, ., 2, 5, ., 1	0.8393	0.992	0.992	N/A	no
Q8TPX5	PSA_METAC	3, ., 4, ., 2, 5, ., 1	0.3934	0.936	0.9473	yes	no
C3N5R0	PSA_SULIA	3, ., 4, ., 2, 5, ., 1	0.4593	0.824	0.8547	yes	no
P0C1G8	PSA4A_ORYSJ	3, ., 4, ., 2, 5, ., 1	0.8393	0.992	0.992	yes	no
Q6M0L9	PSA_METMP	3, ., 4, ., 2, 5, ., 1	0.4317	0.884	0.8532	yes	no
O82530	PSA4_PETHY	3, ., 4, ., 2, 5, ., 1	0.904	0.996	1.0	N/A	no
Q3ZCK9	PSA4_BOVIN	3, ., 4, ., 2, 5, ., 1	0.5966	0.944	0.9042	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.4.25.1	0.993
3rd Layer	3.4.25	0.998

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00007080001	RecName- Full=Proteasome subunit alpha type; EC=3.4.25.1;; The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity (By similarity) (250 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00024499001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (245 aa)			•	•	•	•	•		0.963
	GSVIVG00015420001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (191 aa)			•	•	•	•	•		0.961
	GSVIVG00014791001	SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_1, whole genome shotg [...] (309 aa)				•	•	•	•		0.939
	GSVIVG00023752001	SubName- Full=Putative uncharacterized protein (Chromosome chr7 scaffold_31, whole genome shotg [...] (205 aa)			•	•	•	•	•	•	0.920
	GSVIVG00010470001	SubName- Full=Chromosome chr17 scaffold_263, whole genome shotgun sequence; (386 aa)				•	•	•	•		0.914
	GSVIVG00026350001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (223 aa)			•	•	•	•	•	•	0.894
	GSVIVG00030725001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (250 aa)			•	•	•	•	•	•	0.891
	GSVIVG00035048001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (272 aa)			•	•	•	•	•	•	0.889
	GSVIVG00036762001	SubName- Full=Chromosome chr4 scaffold_83, whole genome shotgun sequence; (440 aa)				•	•	•	•		0.858
	GSVIVG00006696001	SubName- Full=Chromosome chr2 scaffold_176, whole genome shotgun sequence; (267 aa)				•	•	•	•		0.807

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	250
cd03752	213	cd03752, proteasome_alpha_type_4, proteasome_alpha	1e-156
cd01911	209	cd01911, proteasome_alpha, proteasome alpha subuni	1e-120
PTZ00246	253	PTZ00246, PTZ00246, proteasome subunit alpha; Prov	1e-120
PRK03996	241	PRK03996, PRK03996, proteasome subunit alpha; Prov	7e-94
TIGR03633	224	TIGR03633, arc_protsome_A, proteasome endopeptidas	1e-89
cd03756	211	cd03756, proteasome_alpha_archeal, proteasome_alph	3e-89
COG0638	236	COG0638, PRE1, 20S proteasome, alpha and beta subu	9e-77
cd03753	213	cd03753, proteasome_alpha_type_5, proteasome_alpha	5e-72
cd01906	182	cd01906, proteasome_protease_HslV, proteasome_prot	2e-70
cd03755	207	cd03755, proteasome_alpha_type_7, proteasome_alpha	1e-69
pfam00227	188	pfam00227, Proteasome, Proteasome subunit	1e-64
cd03750	227	cd03750, proteasome_alpha_type_2, proteasome_alpha	4e-64
cd03749	211	cd03749, proteasome_alpha_type_1, proteasome_alpha	8e-61
cd03754	215	cd03754, proteasome_alpha_type_6, proteasome_alpha	2e-59
cd03751	212	cd03751, proteasome_alpha_type_3, proteasome_alpha	4e-59
cd01901	164	cd01901, Ntn_hydrolase, The Ntn hydrolases (N-term	5e-45
cd01912	189	cd01912, proteasome_beta, proteasome beta subunit	7e-28
cd03764	188	cd03764, proteasome_beta_archeal, Archeal proteaso	1e-27
TIGR03634	185	TIGR03634, arc_protsome_B, proteasome endopeptidas	6e-25
cd03763	189	cd03763, proteasome_beta_type_7, proteasome beta t	3e-12
cd03758	193	cd03758, proteasome_beta_type_2, proteasome beta t	5e-11
pfam10584	23	pfam10584, Proteasome_A_N, Proteasome subunit A N-	8e-11
smart00948	23	smart00948, Proteasome_A_N, Proteasome subunit A N	3e-10
cd03757	212	cd03757, proteasome_beta_type_1, proteasome beta t	2e-08
TIGR03690	219	TIGR03690, 20S_bact_beta, proteasome, beta subunit	3e-07
cd03762	188	cd03762, proteasome_beta_type_6, proteasome beta t	7e-07
PTZ00488	247	PTZ00488, PTZ00488, Proteasome subunit beta type-5	0.001

>gnl|CDD|239721 cd03752, proteasome_alpha_type_4, proteasome_alpha_type_4

 Score =  432 bits (1112), Expect = e-156
 Identities = 170/213 (79%), Positives = 191/213 (89%)

Query: 3   RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTST 62
           RRYDSRTTIFSPEGRLYQVEYAMEAI +AG+ +GIL+KDG+VL  EKKVTSKLL  S S+
Sbjct: 1   RRYDSRTTIFSPEGRLYQVEYAMEAISHAGTCLGILAKDGIVLAAEKKVTSKLLDQSFSS 60

Query: 63  EKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYT 122
           EK+YKIDDH+ACAVAGI SDANILIN AR+ AQRY Y+YQEP+PVEQLVQ LCD KQGYT
Sbjct: 61  EKIYKIDDHIACAVAGITSDANILINYARLIAQRYLYSYQEPIPVEQLVQRLCDIKQGYT 120

Query: 123 QFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDD 182
           Q+GGLRPFGVSFL+AGWDK+YGFQLY SDPSGNY GWKA AIG NNQAAQS+LKQDYKDD
Sbjct: 121 QYGGLRPFGVSFLYAGWDKHYGFQLYQSDPSGNYSGWKATAIGNNNQAAQSLLKQDYKDD 180

Query: 183 ISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
           ++ EEA+ LA+KVLSKTMDST LTS+KLE A +
Sbjct: 181 MTLEEALALAVKVLSKTMDSTKLTSEKLEFATL 213

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 213

>gnl|CDD|238892 cd01911, proteasome_alpha, proteasome alpha subunit

 Score =  340 bits (874), Expect = e-120
 Identities = 118/211 (55%), Positives = 155/211 (73%), Gaps = 2/211 (0%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T FSPEGRL+QVEYA+EA+ N  +A+GI  KDGVVL  EKKVTSKLL  S S EK
Sbjct: 1   YDRSITTFSPEGRLFQVEYALEAVKNGSTAVGIKGKDGVVLAVEKKVTSKLLDPS-SVEK 59

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           ++KIDDH+ CAVAG+ +DA +L+N ARV+AQ Y Y Y EP+PVE LV+ + D  Q YTQ+
Sbjct: 60  IFKIDDHIGCAVAGLTADARVLVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQY 119

Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDIS 184
           GG+RPFGVS L AG+D+  G QLY +DPSG Y G+KA AIG  +Q A++ L++ YK D++
Sbjct: 120 GGVRPFGVSLLIAGYDEEGGPQLYQTDPSGTYFGYKATAIGKGSQEAKTFLEKRYKKDLT 179

Query: 185 REEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
            EEA++LALK L + ++     +  +E+A V
Sbjct: 180 LEEAIKLALKALKEVLEED-KKAKNIEIAVV 209

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 different alpha and 10 different beta proteasome subunit genes while archaea have one of each. Length = 209

>gnl|CDD|173491 PTZ00246, PTZ00246, proteasome subunit alpha; Provisional

 Score =  341 bits (877), Expect = e-120
 Identities = 142/213 (66%), Positives = 171/213 (80%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTT FSPEGRLYQVEYA+EAI NA   +GIL K+GV+L  +K ++SKLL    
Sbjct: 1   MSRRYDSRTTTFSPEGRLYQVEYALEAINNASLTVGILCKEGVILGADKPISSKLLDPGK 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
             EK+YKID H+ CAVAG+ +DANILIN  R+ AQRY Y Y EP PVEQLV  +CD KQ 
Sbjct: 61  INEKIYKIDSHIFCAVAGLTADANILINQCRLYAQRYRYTYGEPQPVEQLVVQICDLKQS 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGGLRPFGVSFLFAG+D+N G+QLY +DPSGNY GWKA AIG NNQ AQSILKQ++K
Sbjct: 121 YTQFGGLRPFGVSFLFAGYDENLGYQLYHTDPSGNYSGWKATAIGQNNQTAQSILKQEWK 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELA 213
           +D++ E+ + LA KVL+K+MDSTS  +DK+E+ 
Sbjct: 181 EDLTLEQGLLLAAKVLTKSMDSTSPKADKIEVG 213

Length = 253

>gnl|CDD|235192 PRK03996, PRK03996, proteasome subunit alpha; Provisional

 Score =  275 bits (705), Expect = 7e-94
 Identities = 110/233 (47%), Positives = 155/233 (66%), Gaps = 6/233 (2%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   TIFSP+GRLYQVEYA EA+    +A+G+ +KDGVVL  +K++TS L++ S S EK
Sbjct: 10  YDRAITIFSPDGRLYQVEYAREAVKRGTTAVGVKTKDGVVLAVDKRITSPLIEPS-SIEK 68

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           ++KIDDH+  A AG+++DA +LI+ ARV+AQ     Y EP+ VE L + +CD KQ YTQ 
Sbjct: 69  IFKIDDHIGAASAGLVADARVLIDRARVEAQINRLTYGEPIGVETLTKKICDHKQQYTQH 128

Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDIS 184
           GG+RPFGV+ L AG D   G +L+ +DPSG Y  +KA AIGA        L+++YK+D+S
Sbjct: 129 GGVRPFGVALLIAGVDDG-GPRLFETDPSGAYLEYKATAIGAGRDTVMEFLEKNYKEDLS 187

Query: 185 REEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            EEA++LALK L+K  +   L  + +E+A +        K++  S E + K L
Sbjct: 188 LEEAIELALKALAKANEG-KLDPENVEIAYI---DVETKKFRKLSVEEIEKYL 236

Length = 241

>gnl|CDD|163366 TIGR03633, arc_protsome_A, proteasome endopeptidase complex, archaeal, alpha subunit

 Score =  263 bits (675), Expect = 1e-89
 Identities = 103/211 (48%), Positives = 149/211 (70%), Gaps = 3/211 (1%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+GRLYQVEYA EA+    +A+GI +KDGVVL  +K++TSKL++ S S EK
Sbjct: 3   YDRAITVFSPDGRLYQVEYAREAVKRGTTAVGIKTKDGVVLAVDKRITSKLVEPS-SIEK 61

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           ++KIDDH+  A +G+++DA +LI+ AR++AQ     Y EP+ VE L + +CD KQ YTQ 
Sbjct: 62  IFKIDDHIGAATSGLVADARVLIDRARIEAQINRLTYGEPIDVETLAKKICDLKQQYTQH 121

Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDIS 184
           GG+RPFGV+ L AG D   G +L+ +DPSG    +KA AIGA  QA    L+++Y++D+S
Sbjct: 122 GGVRPFGVALLIAGVDDG-GPRLFETDPSGALLEYKATAIGAGRQAVTEFLEKEYREDLS 180

Query: 185 REEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
            +EA++LALK L   ++   LT + +E+A +
Sbjct: 181 LDEAIELALKALYSAVED-KLTPENVEVAYI 210

This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 224

>gnl|CDD|239725 cd03756, proteasome_alpha_archeal, proteasome_alpha_archeal

 Score =  262 bits (672), Expect = 3e-89
 Identities = 107/211 (50%), Positives = 149/211 (70%), Gaps = 3/211 (1%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+GRLYQVEYA EA+    +A+GI  K+GVVL  +K++TSKL++   S EK
Sbjct: 2   YDRAITVFSPDGRLYQVEYAREAVKRGTTALGIKCKEGVVLAVDKRITSKLVEPE-SIEK 60

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +YKIDDHV  A +G+++DA +LI+ ARV+AQ +   Y EP+ VE LV+ +CD KQ YTQ 
Sbjct: 61  IYKIDDHVGAATSGLVADARVLIDRARVEAQIHRLTYGEPIDVEVLVKKICDLKQQYTQH 120

Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDIS 184
           GG+RPFGV+ L AG D   G +L+ +DPSG Y  +KA AIG+  QA    L+++YK+D+S
Sbjct: 121 GGVRPFGVALLIAGVDDG-GPRLFETDPSGAYNEYKATAIGSGRQAVTEFLEKEYKEDMS 179

Query: 185 REEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
            EEA++LALK L   ++    T + +E+A V
Sbjct: 180 LEEAIELALKALYAALEEN-ETPENVEIAYV 209

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 211

>gnl|CDD|223711 COG0638, PRE1, 20S proteasome, alpha and beta subunits [Posttranslational modification, protein turnover, chaperones]

 Score =  231 bits (592), Expect = 9e-77
 Identities = 99/212 (46%), Positives = 142/212 (66%), Gaps = 4/212 (1%)

Query: 3   RRYDSRTTIFSPEGRLYQVEYAMEAIGNAG-SAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
             YD   TIFSPEGRL+QVEYA+EA+   G + +GI  KDGVVL  +K+ TS LL  S++
Sbjct: 1   AGYDRAITIFSPEGRLFQVEYALEAVKRGGTTTVGIKGKDGVVLAADKRATSGLLIASSN 60

Query: 62  TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
            EK++KIDDH+  A+AG+ +DA +L+  AR +AQ Y   Y EP+ VE L + L +  Q Y
Sbjct: 61  VEKIFKIDDHIGMAIAGLAADAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEY 120

Query: 122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD 181
           TQ    RP+GVS L AG D   G +LY +DPSG+Y  +KA AIG+ +Q A   L+++Y++
Sbjct: 121 TQ--SGRPYGVSLLVAGVDDG-GPRLYSTDPSGSYNEYKATAIGSGSQFAYGFLEKEYRE 177

Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELA 213
           D+S EEA++LA+K L   ++  + +   +E+A
Sbjct: 178 DLSLEEAIELAVKALRAAIERDAASGGGIEVA 209

Length = 236

>gnl|CDD|239722 cd03753, proteasome_alpha_type_5, proteasome_alpha_type_5

 Score =  218 bits (558), Expect = 5e-72
 Identities = 103/219 (47%), Positives = 144/219 (65%), Gaps = 14/219 (6%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD     FSPEGRL+QVEYA+EAI    +AIGI +K+GVVL  EK++TS L++ S S EK
Sbjct: 1   YDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIKTKEGVVLAVEKRITSPLMEPS-SVEK 59

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + +IDDH+ CA++G+++DA  LI+ ARV+AQ + + Y EPM VE + Q++ D      QF
Sbjct: 60  IMEIDDHIGCAMSGLIADARTLIDHARVEAQNHRFTYNEPMTVESVTQAVSDL---ALQF 116

Query: 125 GGL--------RPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILK 176
           G          RPFGV+ L AG D+N G QL+ +DPSG +    A AIG+ ++ AQS L+
Sbjct: 117 GEGDDGKKAMSRPFGVALLIAGVDEN-GPQLFHTDPSGTFTRCDAKAIGSGSEGAQSSLQ 175

Query: 177 QDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
           + Y  D++ EEA +LAL +L + M+   L S  +ELA V
Sbjct: 176 EKYHKDMTLEEAEKLALSILKQVMEEK-LNSTNVELATV 213

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 213

>gnl|CDD|238887 cd01906, proteasome_protease_HslV, proteasome_protease_HslV

 Score =  213 bits (546), Expect = 2e-70
 Identities = 85/184 (46%), Positives = 118/184 (64%), Gaps = 2/184 (1%)

Query: 32  GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTAR 91
            + +GI  KDGVVL  +K+VTS LL  S++ EK++KIDDH+ CA AG+ +DA  L+   R
Sbjct: 1   TTIVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVERLR 60

Query: 92  VQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSD 151
            +AQ Y   Y EP+PVE L + L +    YTQ   LRP GVS L AG D+  G QLY  D
Sbjct: 61  KEAQLYRLRYGEPIPVEALAKLLANLLYEYTQS--LRPLGVSLLVAGVDEEGGPQLYSVD 118

Query: 152 PSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLE 211
           PSG+Y  +KA AIG+ +Q A  IL++ YK D++ EEA++LALK L   ++    +   +E
Sbjct: 119 PSGSYIEYKATAIGSGSQYALGILEKLYKPDMTLEEAIELALKALKSALERDLYSGGNIE 178

Query: 212 LAEV 215
           +A +
Sbjct: 179 VAVI 182

This group contains the eukaryotic proteosome alpha and beta subunits and the prokaryotic protease hslV subunit. Proteasomes are large multimeric self-compartmentalizing proteases, involved in the clearance of misfolded proteins, the breakdown of regulatory proteins, and the processing of proteins such as the preparation of peptides for immune presentation. Two main proteasomal types are distinguished by their different tertiary structures: the eukaryotic/archeal 20S proteasome and the prokaryotic proteasome-like heat shock protein encoded by heat shock locus V, hslV. The proteasome core particle is a highly conserved cylindrical structure made up of non-identical subunits that have their active sites on the inner walls of a large central cavity. The proteasome subunits of bacteria, archaea, and eukaryotes all share a conserved Ntn (N terminal nucleophile) hydrolase fold and a catalytic mechanism involving an N-terminal nucleophilic threonine that is exposed by post-translational processing of an inactive propeptide. Length = 182

>gnl|CDD|239724 cd03755, proteasome_alpha_type_7, proteasome_alpha_type_7

 Score =  212 bits (542), Expect = 1e-69
 Identities = 85/200 (42%), Positives = 132/200 (66%), Gaps = 1/200 (0%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+G L+QVEYA EA+    +A+G+  KD VVL  EKK  +KL Q   +  K
Sbjct: 1   YDRAITVFSPDGHLFQVEYAQEAVRKGTTAVGVRGKDCVVLGVEKKSVAKL-QDPRTVRK 59

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +DDHV  A AG+ +DA +LIN AR++ Q +    ++P+ VE + + +   +Q YTQ 
Sbjct: 60  ICMLDDHVCLAFAGLTADARVLINRARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQS 119

Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDIS 184
           GG+RPFG+S L  G+D +   +LY +DPSG Y  WKA AIG N++  +  L+++YK++++
Sbjct: 120 GGVRPFGISTLIVGFDPDGTPRLYQTDPSGTYSAWKANAIGRNSKTVREFLEKNYKEEMT 179

Query: 185 REEAVQLALKVLSKTMDSTS 204
           R++ ++LA+K L + + S S
Sbjct: 180 RDDTIKLAIKALLEVVQSGS 199

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 207

>gnl|CDD|215805 pfam00227, Proteasome, Proteasome subunit

 Score =  199 bits (508), Expect = 1e-64
 Identities = 78/187 (41%), Positives = 118/187 (63%), Gaps = 2/187 (1%)

Query: 30  NAGSAIGILSKDGVVLVGEKKVTSK-LLQTSTSTEKMYKIDDHVACAVAGIMSDANILIN 88
              + +GI  KDGVVL  +K+ T    L +  + EK++KIDDH+  A AG+ +DA  L++
Sbjct: 3   TGTTIVGIKGKDGVVLAADKRATRGSKLLSKDTVEKIFKIDDHIGMAFAGLAADAQTLVD 62

Query: 89  TARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLY 148
            AR +AQ Y   Y  P+ VE L + + D  Q YTQ+ G RP+GVS L AG+D++ G  LY
Sbjct: 63  YARAEAQLYRLRYGRPISVE-LAKRIADKLQAYTQYSGRRPYGVSLLIAGYDEDGGPHLY 121

Query: 149 MSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSD 208
             DPSG+   +KA AIG+ +Q A   L++ YK D++ EEAV+LA+K L + ++  +L+  
Sbjct: 122 SIDPSGSVIEYKATAIGSGSQYAYGFLEKLYKPDMTLEEAVELAVKALKEAIERDALSGG 181

Query: 209 KLELAEV 215
            +E+A +
Sbjct: 182 NIEVAVI 188

The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria. The second is call beta-proteobacteria proteasome homologue (BPH). Length = 188

>gnl|CDD|239719 cd03750, proteasome_alpha_type_2, proteasome_alpha_type_2

 Score =  199 bits (508), Expect = 4e-64
 Identities = 86/204 (42%), Positives = 124/204 (60%), Gaps = 3/204 (1%)

Query: 10  TIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKID 69
           T FSP G+L Q+EYA+ A+ +   ++GI + +GVVL  EKKV S L+  S S  K+ +I 
Sbjct: 6   TTFSPSGKLVQIEYALAAVSSGAPSVGIKAANGVVLATEKKVPSPLIDES-SVHKVEQIT 64

Query: 70  DHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRP 129
            H+    +G+  D  +L+  AR  AQ+Y   Y EP+PV QLV+ +    Q YTQ GG+RP
Sbjct: 65  PHIGMVYSGMGPDFRVLVKKARKIAQQYYLVYGEPIPVSQLVREIASVMQEYTQSGGVRP 124

Query: 130 FGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAV 189
           FGVS L AGWD+  G  LY  DPSG+Y  WKA AIG N   A++ L++ Y +D+  E+A+
Sbjct: 125 FGVSLLIAGWDEG-GPYLYQVDPSGSYFTWKATAIGKNYSNAKTFLEKRYNEDLELEDAI 183

Query: 190 QLALKVLSKTMDSTSLTSDKLELA 213
             A+  L +  +   +T   +E+ 
Sbjct: 184 HTAILTLKEGFE-GQMTEKNIEIG 206

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 227

>gnl|CDD|239718 cd03749, proteasome_alpha_type_1, proteasome_alpha_type_1

 Score =  190 bits (484), Expect = 8e-61
 Identities = 85/214 (39%), Positives = 135/214 (63%), Gaps = 7/214 (3%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD+  T +SP+GRL+QVEYAMEA+    + +G+ SK   VLV  K+ TS+L   S+  +K
Sbjct: 1   YDTDVTTWSPQGRLFQVEYAMEAVKQGSATVGLKSKTHAVLVALKRATSEL---SSYQKK 57

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           ++K+DDH+  A+AG+ +DA +L    R +   Y + Y  P+PV +LV  + +  Q  TQ 
Sbjct: 58  IFKVDDHIGIAIAGLTADARVLSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQR 117

Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK--DD 182
            G RP+GV  L AG+D++ G  L+ + PSGNY  +KA +IGA +Q+A++ L++ ++  +D
Sbjct: 118 YGRRPYGVGLLIAGYDES-GPHLFQTCPSGNYFEYKATSIGARSQSARTYLERHFEEFED 176

Query: 183 ISREEAVQLALKVLSKTMDSTS-LTSDKLELAEV 215
            S EE ++ AL+ L +T+     LT   + +A V
Sbjct: 177 CSLEELIKHALRALRETLPGEQELTIKNVSIAIV 210

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 211

>gnl|CDD|239723 cd03754, proteasome_alpha_type_6, proteasome_alpha_type_6

 Score =  187 bits (476), Expect = 2e-59
 Identities = 86/216 (39%), Positives = 127/216 (58%), Gaps = 7/216 (3%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAG-SAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
           +D   TIFSPEGRLYQVEYA +A+ NAG +++ +  KD  V+V +KKV  KL+  ST T 
Sbjct: 2   FDRHITIFSPEGRLYQVEYAFKAVKNAGLTSVAVRGKDCAVVVTQKKVPDKLIDPSTVTH 61

Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
            +++I D + C + G+++D+   +  AR +A  + Y Y   MPV+ L + + D  Q YTQ
Sbjct: 62  -LFRITDEIGCVMTGMIADSRSQVQRARYEAAEFKYKYGYEMPVDVLAKRIADINQVYTQ 120

Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDD- 182
              +RP GVS +  G D+  G QLY  DP+G + G+KA A G   Q A + L++  K   
Sbjct: 121 HAYMRPLGVSMILIGIDEELGPQLYKCDPAGYFAGYKATAAGVKEQEATNFLEKKLKKKP 180

Query: 183 ---ISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
               S EE V+LA+  L  T+ ST   + ++E+  V
Sbjct: 181 DLIESYEETVELAISCLQ-TVLSTDFKATEIEVGVV 215

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 215

>gnl|CDD|239720 cd03751, proteasome_alpha_type_3, proteasome_alpha_type_3

 Score =  185 bits (473), Expect = 4e-59
 Identities = 82/197 (41%), Positives = 123/197 (62%), Gaps = 2/197 (1%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   + FSP+GR++QVEYA +A+ N+G+AIGI  KDGVVL  EK VTSKL +   S ++
Sbjct: 4   YDLSASTFSPDGRVFQVEYANKAVENSGTAIGIRCKDGVVLAVEKLVTSKLYEPG-SNKR 62

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           ++ +D H+  AVAG+++D   L++ AR +A+ Y   Y  P+PV+ L   +      YT +
Sbjct: 63  IFNVDRHIGIAVAGLLADGRHLVSRAREEAENYRDNYGTPIPVKVLADRVAMYMHAYTLY 122

Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDIS 184
             +RPFG S L  G+D + G QLYM +PSG   G+   AIG   QAA++ L++    +++
Sbjct: 123 SSVRPFGCSVLLGGYDSD-GPQLYMIEPSGVSYGYFGCAIGKGKQAAKTELEKLKFSELT 181

Query: 185 REEAVQLALKVLSKTMD 201
             EAV+ A K++    D
Sbjct: 182 CREAVKEAAKIIYIVHD 198

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 212

>gnl|CDD|238884 cd01901, Ntn_hydrolase, The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid

 Score =  148 bits (375), Expect = 5e-45
 Identities = 65/167 (38%), Positives = 94/167 (56%), Gaps = 5/167 (2%)

Query: 32  GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTAR 91
            +++ I  K GVVL  +K+++S L    +   K+ K +D +A  +AG+ +DA  L+   R
Sbjct: 1   STSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLR 60

Query: 92  VQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSD 151
              Q Y   Y EP+ V  L + L    Q YTQ    RPFGV+ + AG D+  G  LY  D
Sbjct: 61  EALQLYRLRYGEPISVVALAKELAKLLQVYTQ---GRPFGVNLIVAGVDEGGG-NLYYID 116

Query: 152 PSGNYGGW-KAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLS 197
           PSG       A A G+ +Q A+S+L++ YK D++ EEAV+LALK L 
Sbjct: 117 PSGPVIENPGAVATGSRSQRAKSLLEKLYKPDMTLEEAVELALKALK 163

N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences. Length = 164

>gnl|CDD|238893 cd01912, proteasome_beta, proteasome beta subunit

 Score =  104 bits (263), Expect = 7e-28
 Identities = 49/185 (26%), Positives = 89/185 (48%), Gaps = 10/185 (5%)

Query: 32  GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTAR 91
            + +GI  KDGVVL  + + ++  L  S + +K++KI D++    AG  +D   L    +
Sbjct: 1   TTIVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISDNILLGTAGSAADTQALTRLLK 60

Query: 92  VQAQRYTYAYQEPMPVE---QLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLY 148
              + Y       + V+    L+ ++  + +G+       P+ VS +  G DK  G  LY
Sbjct: 61  RNLRLYELRNGRELSVKAAANLLSNILYSYRGF-------PYYVSLIVGGVDKGGGPFLY 113

Query: 149 MSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSD 208
             DP G+       A G+ ++ A  IL + YK D++ EEAV+L  K +   ++    +  
Sbjct: 114 YVDPLGSLIEAPFVATGSGSKYAYGILDRGYKPDMTLEEAVELVKKAIDSAIERDLSSGG 173

Query: 209 KLELA 213
            +++A
Sbjct: 174 GVDVA 178

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 189

>gnl|CDD|239733 cd03764, proteasome_beta_archeal, Archeal proteasome, beta subunit

 Score =  103 bits (260), Expect = 1e-27
 Identities = 53/180 (29%), Positives = 94/180 (52%), Gaps = 5/180 (2%)

Query: 34  AIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQ 93
            +GI+ KDGVVL  +K+ +      S + +K+++IDD +A  +AG + DA  L+   + +
Sbjct: 3   TVGIVCKDGVVLAADKRASMGNFIASKNVKKIFQIDDKIAMTIAGSVGDAQSLVRILKAE 62

Query: 94  AQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPS 153
           A+ Y      PM ++ L   L +       F    P+ V  L  G D+  G  LY  DP 
Sbjct: 63  ARLYELRRGRPMSIKALATLLSNILNSSKYF----PYIVQLLIGGVDEE-GPHLYSLDPL 117

Query: 154 GNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELA 213
           G+    K  A G+ +  A  +L+ +YK+D++ EEA +LA++ +   ++  S + D +++ 
Sbjct: 118 GSIIEDKYTATGSGSPYAYGVLEDEYKEDMTVEEAKKLAIRAIKSAIERDSASGDGIDVV 177

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme for non-lysosomal protein degradation in both the cytosol and the nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are both members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 188

>gnl|CDD|234287 TIGR03634, arc_protsome_B, proteasome endopeptidase complex, archaeal, beta subunit

 Score = 97.3 bits (243), Expect = 6e-25
 Identities = 53/182 (29%), Positives = 94/182 (51%), Gaps = 5/182 (2%)

Query: 34  AIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQ 93
            +GI  KDGVVL  +K+ +      S + +K+++IDD++A  +AG + DA  L+   + +
Sbjct: 4   TVGIKCKDGVVLAADKRASMGNFVASKNAKKVFQIDDYIAMTIAGSVGDAQSLVRILKAE 63

Query: 94  AQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPS 153
           A+ Y      PM V+ L   L +       F    PF V  L  G D+  G  LY  DP+
Sbjct: 64  AKLYELRRGRPMSVKALATLLSNILNSNRFF----PFIVQLLVGGVDEE-GPHLYSLDPA 118

Query: 154 GNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELA 213
           G        A G+ +  A  +L+ +Y++D+S EEA +LA++ +   ++    + + +++A
Sbjct: 119 GGIIEDDYTATGSGSPVAYGVLEDEYREDMSVEEAKKLAVRAIKSAIERDVASGNGIDVA 178

Query: 214 EV 215
            +
Sbjct: 179 VI 180

This protein family describes the archaeal proteasome beta subunit, homologous to both the alpha subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 185

>gnl|CDD|239732 cd03763, proteasome_beta_type_7, proteasome beta type-7 subunit

 Score = 63.0 bits (154), Expect = 3e-12
 Identities = 40/161 (24%), Positives = 68/161 (42%), Gaps = 12/161 (7%)

Query: 35  IGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQA 94
           +G++ KDGVVL  + + T   +    + EK++ I  ++ C  AG  +D   + N      
Sbjct: 4   VGVVFKDGVVLGADTRATEGPIVADKNCEKIHYIAPNIYCCGAGTAADTEAVTNMISSNL 63

Query: 95  QRYTYAYQEPMPVEQLVQSLCDT---KQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSD 151
           + +         V   +  L       QG+         G + +  G D   G  LY   
Sbjct: 64  ELHRLNTGRKPRVVTALTMLKQHLFRYQGH--------IGAALVLGGVD-YTGPHLYSIY 114

Query: 152 PSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLA 192
           P G+        +G+ + AA S+L+  YK D++ EEA +L 
Sbjct: 115 PHGSTDKLPFVTMGSGSLAAMSVLEDRYKPDMTEEEAKKLV 155

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 189

>gnl|CDD|239727 cd03758, proteasome_beta_type_2, proteasome beta type-2 subunit

 Score = 59.5 bits (145), Expect = 5e-11
 Identities = 49/175 (28%), Positives = 72/175 (41%), Gaps = 34/175 (19%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + IGI  KD V+L  +      +L      +K+YK+ DH   A +G   D        R+
Sbjct: 3   TLIGIKGKDFVILAADTSAARSILVLKDDEDKIYKLSDHKLMACSGEAGD--------RL 54

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF-------------GGLR---PFGVSFLF 136
           Q   Y    Q+ + + ++       + GY                  LR   P+ V+ L 
Sbjct: 55  QFAEYI---QKNIQLYKM-------RNGYELSPKAAANFTRRELAESLRSRTPYQVNLLL 104

Query: 137 AGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL 191
           AG+DK  G  LY  D  G       AA G       SIL + YK D++ EEA++L
Sbjct: 105 AGYDKVEGPSLYYIDYLGTLVKVPYAAHGYGAYFCLSILDRYYKPDMTVEEALEL 159

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis.Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 193

>gnl|CDD|204518 pfam10584, Proteasome_A_N, Proteasome subunit A N-terminal signature

 Score = 55.1 bits (134), Expect = 8e-11
 Identities = 16/23 (69%), Positives = 19/23 (82%)

Query: 5  YDSRTTIFSPEGRLYQVEYAMEA 27
          YD   T FSP+GRL+QVEYAM+A
Sbjct: 1  YDRSLTTFSPDGRLFQVEYAMKA 23

This domain is conserved in the A subunits of the proteasome complex proteins. Length = 23

>gnl|CDD|198016 smart00948, Proteasome_A_N, Proteasome subunit A N-terminal signature Add an annotation

 Score = 53.7 bits (130), Expect = 3e-10
 Identities = 17/23 (73%), Positives = 19/23 (82%)

Query: 5  YDSRTTIFSPEGRLYQVEYAMEA 27
          YD   T FSP+GRL+QVEYAMEA
Sbjct: 1  YDRSLTTFSPDGRLFQVEYAMEA 23

This domain is conserved in the A subunits of the proteasome complex proteins. Length = 23

>gnl|CDD|239726 cd03757, proteasome_beta_type_1, proteasome beta type-1 subunit

 Score = 53.0 bits (128), Expect = 2e-08
 Identities = 44/192 (22%), Positives = 78/192 (40%), Gaps = 13/192 (6%)

Query: 30  NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINT 89
           N G+ + I   D  V+ G+ +++      S  + K++K+ D      +G  +D   L   
Sbjct: 7   NGGTVLAIAGNDFAVIAGDTRLSEGYSILSRDSPKIFKLTDKCVLGSSGFQADILALTKR 66

Query: 90  ARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYM 149
            + + + Y Y++ + M  E + Q L         F    P+ V  + AG D+     +Y 
Sbjct: 67  LKARIKMYKYSHNKEMSTEAIAQLLSTILYSRRFF----PYYVFNILAGIDEEGKGVVYS 122

Query: 150 SDPSGNYGGWKAAAIGANNQAAQSIL---------KQDYKDDISREEAVQLALKVLSKTM 200
            DP G+Y     +A G+ +   Q +L             +  +S EEAV L     +   
Sbjct: 123 YDPVGSYERETYSAGGSASSLIQPLLDNQVGRKNQNNVERTPLSLEEAVSLVKDAFTSAA 182

Query: 201 DSTSLTSDKLEL 212
           +    T D LE+
Sbjct: 183 ERDIYTGDSLEI 194

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 212

>gnl|CDD|163402 TIGR03690, 20S_bact_beta, proteasome, beta subunit, bacterial type

 Score = 49.3 bits (118), Expect = 3e-07
 Identities = 41/169 (24%), Positives = 80/169 (47%), Gaps = 3/169 (1%)

Query: 40  KDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTY 99
             GV++ G+++ T   +  S   EK+Y  D++ A  +AG    A  L+   +V+ + Y  
Sbjct: 11  PGGVLMAGDRRATQGNMIASRDVEKVYPTDEYSAVGIAGTAGLAIELVRLFQVELEHYEK 70

Query: 100 AYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGF-QLYMSDPSG-NYG 157
               P+ ++     L    +G      ++   V  L AG+D + G  +++  D +G  Y 
Sbjct: 71  IEGVPLTLDGKANRLAAMVRGNLPAA-MQGLAVVPLLAGYDLDAGAGRIFSYDVTGGRYE 129

Query: 158 GWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLT 206
                A+G+ +  A+  LK+ Y  D+  ++A+++A++ L    D  S T
Sbjct: 130 ERGYHAVGSGSVFAKGALKKLYSPDLDEDDALRVAVEALYDAADDDSAT 178

Members of this family are the beta subunit of the 20S proteasome as found in Actinobacteria such as Mycobacterium, Rhodococcus, and Streptomyces. In Streptomyces, maturation during proteasome assembly was shown to remove a 53-amino acid propeptide. Most of the length of the propeptide is not included in this model [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 219

>gnl|CDD|239731 cd03762, proteasome_beta_type_6, proteasome beta type-6 subunit

 Score = 48.0 bits (115), Expect = 7e-07
 Identities = 39/175 (22%), Positives = 71/175 (40%), Gaps = 13/175 (7%)

Query: 35  IGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQA 94
           I +    GVVL  + + ++     +  T+K+ ++ D + C  +G  +D   + +  R   
Sbjct: 4   IAVEYDGGVVLGADSRTSTGSYVANRVTDKLTQLHDRIYCCRSGSAADTQAIADYVRYYL 63

Query: 95  QRYTYAYQEPMPVE---QLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSD 151
             ++    EP  V+    L ++LC     Y     L       + AGWD+  G Q+Y   
Sbjct: 64  DMHSIELGEPPLVKTAASLFKNLC-----YNYKEMLS---AGIIVAGWDEQNGGQVYSIP 115

Query: 152 PSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTM--DSTS 204
             G       A  G+ +      +  +YK  ++ EE ++     LS  M  D +S
Sbjct: 116 LGGMLIRQPFAIGGSGSTYIYGYVDANYKPGMTLEECIKFVKNALSLAMSRDGSS 170

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. Length = 188

>gnl|CDD|185666 PTZ00488, PTZ00488, Proteasome subunit beta type-5; Provisional

 Score = 39.2 bits (91), Expect = 0.001
 Identities = 34/164 (20%), Positives = 65/164 (39%), Gaps = 5/164 (3%)

Query: 28  IGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILI 87
             +  + +      G+++  + K T+     S S +K+ +I+  +   +AG  +D +   
Sbjct: 36  FAHGTTTLAFKYGGGIIIAVDSKATAGPYIASQSVKKVIEINPTLLGTMAGGAADCSFWE 95

Query: 88  NTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQL 147
               +Q + Y     E + V    + L +    Y   G      +  +  GWDK  G  L
Sbjct: 96  RELAMQCRLYELRNGELISVAAASKILANIVWNYKGMG----LSMGTMICGWDKK-GPGL 150

Query: 148 YMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL 191
           +  D  G        + G+ +  A  +L   +K D++ EEA  L
Sbjct: 151 FYVDNDGTRLHGNMFSCGSGSTYAYGVLDAGFKWDLNDEEAQDL 194

Length = 247

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	250
PTZ00246	253	proteasome subunit alpha; Provisional	100.0
cd03750	227	proteasome_alpha_type_2 proteasome_alpha_type_2. T	100.0
PRK03996	241	proteasome subunit alpha; Provisional	100.0
cd03752	213	proteasome_alpha_type_4 proteasome_alpha_type_4. T	100.0
KOG0178	249	consensus 20S proteasome, regulatory subunit alpha	100.0
TIGR03633	224	arc_protsome_A proteasome endopeptidase complex, a	100.0
cd03751	212	proteasome_alpha_type_3 proteasome_alpha_type_3. T	100.0
KOG0176	241	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03755	207	proteasome_alpha_type_7 proteasome_alpha_type_7. T	100.0
cd03749	211	proteasome_alpha_type_1 proteasome_alpha_type_1. T	100.0
COG0638	236	PRE1 20S proteasome, alpha and beta subunits [Post	100.0
cd03756	211	proteasome_alpha_archeal proteasome_alpha_archeal.	100.0
cd03754	215	proteasome_alpha_type_6 proteasome_alpha_type_6. T	100.0
cd01911	209	proteasome_alpha proteasome alpha subunit. The 20S	100.0
KOG0184	254	consensus 20S proteasome, regulatory subunit alpha	100.0
cd03753	213	proteasome_alpha_type_5 proteasome_alpha_type_5. T	100.0
KOG0183	249	consensus 20S proteasome, regulatory subunit alpha	100.0
KOG0181	233	consensus 20S proteasome, regulatory subunit alpha	100.0
KOG0182	246	consensus 20S proteasome, regulatory subunit alpha	100.0
KOG0863	264	consensus 20S proteasome, regulatory subunit alpha	100.0
TIGR03690	219	20S_bact_beta proteasome, beta subunit, bacterial	100.0
PTZ00488	247	Proteasome subunit beta type-5; Provisional	100.0
TIGR03691	228	20S_bact_alpha proteasome, alpha subunit, bacteria	100.0
cd03758	193	proteasome_beta_type_2 proteasome beta type-2 subu	100.0
cd03759	195	proteasome_beta_type_3 proteasome beta type-3 subu	100.0
cd03760	197	proteasome_beta_type_4 proteasome beta type-4 subu	100.0
cd03761	188	proteasome_beta_type_5 proteasome beta type-5 subu	100.0
TIGR03634	185	arc_protsome_B proteasome endopeptidase complex, a	100.0
cd03757	212	proteasome_beta_type_1 proteasome beta type-1 subu	100.0
cd03764	188	proteasome_beta_archeal Archeal proteasome, beta s	100.0
cd03765	236	proteasome_beta_bacterial Bacterial proteasome, be	100.0
cd03762	188	proteasome_beta_type_6 proteasome beta type-6 subu	100.0
cd03763	189	proteasome_beta_type_7 proteasome beta type-7 subu	100.0
cd01912	189	proteasome_beta proteasome beta subunit. The 20S p	100.0
PF00227	190	Proteasome: Proteasome subunit; InterPro: IPR00135	100.0
cd01906	182	proteasome_protease_HslV proteasome_protease_HslV.	100.0
KOG0177	200	consensus 20S proteasome, regulatory subunit beta	100.0
KOG0179	235	consensus 20S proteasome, regulatory subunit beta	100.0
KOG0174	224	consensus 20S proteasome, regulatory subunit beta	100.0
KOG0175	285	consensus 20S proteasome, regulatory subunit beta	100.0
KOG0185	256	consensus 20S proteasome, regulatory subunit beta	100.0
KOG0173	271	consensus 20S proteasome, regulatory subunit beta	100.0
PRK05456	172	ATP-dependent protease subunit HslV; Provisional	100.0
KOG0180	204	consensus 20S proteasome, regulatory subunit beta	100.0
cd01913	171	protease_HslV Protease HslV and the ATPase/chapero	100.0
TIGR03692	171	ATP_dep_HslV ATP-dependent protease HslVU, peptida	99.97
cd01901	164	Ntn_hydrolase The Ntn hydrolases (N-terminal nucle	99.97
COG3484	255	Predicted proteasome-type protease [Posttranslatio	99.69
COG5405	178	HslV ATP-dependent protease HslVU (ClpYQ), peptida	99.59
PF10584	23	Proteasome_A_N: Proteasome subunit A N-terminal si	99.56
PF09894	194	DUF2121: Uncharacterized protein conserved in arch	97.18
COG4079	293	Uncharacterized protein conserved in archaea [Func	96.29
KOG3361	157	consensus Iron binding protein involved in Fe-S cl	81.01

>PTZ00246 proteasome subunit alpha; Provisional

Probab=100.00  E-value=2.1e-63  Score=425.31  Aligned_cols=247  Identities=59%  Similarity=0.932  Sum_probs=234.1

Q ss_pred             CCCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         1 ~~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      |+++||+++|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.++++++++++.+||++|+++++|+++|..
T Consensus         1 ~~~~yd~~~~~fsp~Grl~QvEYA~~av~~g~t~Igik~~dgVvlaad~r~s~~~~~~~~~~~KI~~I~~~i~~~~sG~~   80 (253)
T PTZ00246          1 MSRRYDSRTTTFSPEGRLYQVEYALEAINNASLTVGILCKEGVILGADKPISSKLLDPGKINEKIYKIDSHIFCAVAGLT   80 (253)
T ss_pred             CCCccCCCCceECCCCEEhHHHHHHHHHHhCCCEEEEEECCEEEEEEecCCCCcCccCCCCcccEEEecCCEEEEEEEcH
Confidence            99999999999999999999999999999999999999999999999999999999988778999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce
Q 025640           81 SDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK  160 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~  160 (250)
                      +|++.+.+.+|.++..|++.++.+++++.+++.++..+|.|+|+++.|||+|++||+|||++.||+||.+||+|++.+++
T Consensus        81 ~D~~~l~~~~r~~~~~~~~~~~~~~~v~~l~~~l~~~~q~~~~~~~~rP~~v~~li~G~D~~~gp~Ly~~D~~Gs~~~~~  160 (253)
T PTZ00246         81 ADANILINQCRLYAQRYRYTYGEPQPVEQLVVQICDLKQSYTQFGGLRPFGVSFLFAGYDENLGYQLYHTDPSGNYSGWK  160 (253)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccCCEEEEEEEEeCCCCcEEEEECCCCCEecce
Confidence            99999999999999999999999999999999999999999999999999999999999976689999999999999999


Q ss_pred             EEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCC-ceeEEECCHHHHHHHHHH
Q 025640          161 AAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSG-KVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       161 ~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~-~~~~~~~~~~ei~~~~~~  239 (250)
                      ++|+|.|+.+++++||+.|+++|+++||++++++||+.+.++++.+++.++|++|+++++. ...|++++++||+.++.+
T Consensus       161 ~~a~G~gs~~~~~~Le~~~~~~ms~eeai~l~~~al~~~~~~d~~s~~~vev~ii~~~~~~~~~~~~~l~~~ei~~~l~~  240 (253)
T PTZ00246        161 ATAIGQNNQTAQSILKQEWKEDLTLEQGLLLAAKVLTKSMDSTSPKADKIEVGILSHGETDGEPIQKMLSEKEIAELLKK  240 (253)
T ss_pred             EEEECCCcHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEecCCcCCCCCeEECCHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999987521 124899999999999999


Q ss_pred             hCCCCccc
Q 025640          240 HGVTQPAA  247 (250)
Q Consensus       240 ~~~~~~~~  247 (250)
                      +.+....|
T Consensus       241 ~~~~~~~~  248 (253)
T PTZ00246        241 VTQEYAKE  248 (253)
T ss_pred             Hhhhhhhh
Confidence            87665444

>cd03750 proteasome_alpha_type_2 proteasome_alpha_type_2

Probab=100.00  E-value=3.8e-60  Score=399.28  Aligned_cols=226  Identities=39%  Similarity=0.681  Sum_probs=215.2

Q ss_pred             CCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHH
Q 025640            5 YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDAN   84 (250)
Q Consensus         5 yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~   84 (250)
                      ||+.+|+|||||||+|||||.+|+++|+|+|||+++||||||+|++.++++ ..+++.+||++|++|++|+++|..+|++
T Consensus         1 yd~~~t~fsp~Grl~QveyA~~av~~G~t~igik~~dgVvlaad~~~~~~l-~~~~~~~KI~~I~~~i~~~~sG~~~D~~   79 (227)
T cd03750           1 YSFSLTTFSPSGKLVQIEYALAAVSSGAPSVGIKAANGVVLATEKKVPSPL-IDESSVHKVEQITPHIGMVYSGMGPDFR   79 (227)
T ss_pred             CCCCCceECCCCeEhHHHHHHHHHHcCCCEEEEEeCCEEEEEEeecCCccc-cCCCCcceEEEEcCCEEEEEeEcHHhHH
Confidence            899999999999999999999999999999999999999999999998654 4556789999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEE
Q 025640           85 ILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAI  164 (250)
Q Consensus        85 ~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~  164 (250)
                      .+.+.++.++..|++.++.+++++.+++.|++.+|.++++++.||++|++||+|||+. ||+||.+||+|++.+++++|+
T Consensus        80 ~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v~~li~G~D~~-g~~Ly~~d~~G~~~~~~~~a~  158 (227)
T cd03750          80 VLVKKARKIAQQYYLVYGEPIPVSQLVREIASVMQEYTQSGGVRPFGVSLLIAGWDEG-GPYLYQVDPSGSYFTWKATAI  158 (227)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCCCChheEEEEEEEeCC-CCEEEEECCCCCEEeeeEEEE
Confidence            9999999999999999999999999999999999999999999999999999999974 899999999999999999999


Q ss_pred             eCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 025640          165 GANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL  237 (250)
Q Consensus       165 G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~  237 (250)
                      |.|+.+++++||++|+++||++||++++++||+.+.+++ .++.+++|++|++++    .++.++++||+.++
T Consensus       159 G~g~~~~~~~Le~~~~~~ms~eeai~l~~~~l~~~~~~~-l~~~~iev~iv~~~~----~~~~~~~~ei~~~~  226 (227)
T cd03750         159 GKNYSNAKTFLEKRYNEDLELEDAIHTAILTLKEGFEGQ-MTEKNIEIGICGETK----GFRLLTPAEIKDYL  226 (227)
T ss_pred             CCCCHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhccc-CCCCcEEEEEEECCC----CEEECCHHHHHHHh
Confidence            999999999999999999999999999999999999874 699999999999863    38999999999886

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>PRK03996 proteasome subunit alpha; Provisional

Probab=100.00  E-value=6.4e-59  Score=395.20  Aligned_cols=232  Identities=47%  Similarity=0.767  Sum_probs=220.5

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      .+||+++|+|||||||+|||||.+|+++|+|+|||+++||||||+|++.++++. ..++.+||++|+++++|++||..+|
T Consensus         8 ~~y~~~~~~fsp~Gr~~Q~eya~~av~~G~t~igik~~dgVvlaad~r~~~~~~-~~~~~~KI~~I~~~i~~~~sG~~~D   86 (241)
T PRK03996          8 MGYDRAITIFSPDGRLYQVEYAREAVKRGTTAVGVKTKDGVVLAVDKRITSPLI-EPSSIEKIFKIDDHIGAASAGLVAD   86 (241)
T ss_pred             cccCCCCceECCCCeEhHHHHHHHHHHhCCCEEEEEeCCEEEEEEeccCCCccc-CCCccceEEEEcCCEEEEEcccHHH
Confidence            489999999999999999999999999999999999999999999999986654 4457899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+.++.++..|++.++.+++++.+++.++..+|.|+++++.|||+|++||||||+ .||+||.+||+|++.+++++
T Consensus        87 ~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~~~~~~~rP~~~~~ilaG~d~-~gp~Ly~id~~G~~~~~~~~  165 (241)
T PRK03996         87 ARVLIDRARVEAQINRLTYGEPIGVETLTKKICDHKQQYTQHGGVRPFGVALLIAGVDD-GGPRLFETDPSGAYLEYKAT  165 (241)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhcCCCCccchheEEEEEEEeC-CcCEEEEECCCCCeecceEE
Confidence            99999999999999999999999999999999999999999999999999999999997 48999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 025640          163 AIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH  240 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~  240 (250)
                      |+|.++.+++++|++.|+++|+++||++++++||+.+.++ ..++++++|++|++++.   .++.++++||+.+++++
T Consensus       166 a~G~g~~~~~~~Le~~~~~~~s~eeai~l~~~al~~~~~~-~~~~~~i~i~ii~~~~~---~~~~~~~~ei~~~~~~~  239 (241)
T PRK03996        166 AIGAGRDTVMEFLEKNYKEDLSLEEAIELALKALAKANEG-KLDPENVEIAYIDVETK---KFRKLSVEEIEKYLEKL  239 (241)
T ss_pred             EECCCcHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHhcc-CCCCCcEEEEEEECCCC---cEEECCHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999875 77899999999999873   48999999999999875

>cd03752 proteasome_alpha_type_4 proteasome_alpha_type_4

Probab=100.00  E-value=3.6e-59  Score=389.84  Aligned_cols=213  Identities=80%  Similarity=1.232  Sum_probs=207.3

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      ++||+++|+|||||||+|||||.||+++|+|+|||+++||||||+|+|.++++++.+++.+||++|+++++|++||..+|
T Consensus         1 ~~yd~~~~~fsp~Grl~Qveya~~a~~~G~t~igi~~~dgVvla~d~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D   80 (213)
T cd03752           1 RRYDSRTTIFSPEGRLYQVEYAMEAISHAGTCLGILAKDGIVLAAEKKVTSKLLDQSFSSEKIYKIDDHIACAVAGITSD   80 (213)
T ss_pred             CCcCCCCceECCCCEEhHHHhHHHHHhcCCCEEEEEeCCEEEEEEEeccCCcccCCCcCcceEEEecCCEEEEEecChHh
Confidence            47999999999999999999999999999999999999999999999999999988878999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+.++.++..|++.++++++++.+++.|+..+|.|++.++.|||+|++||+|||+..||+||.+||+|++.+++++
T Consensus        81 ~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~RP~~v~~li~G~D~~~g~~ly~~d~~G~~~~~~~~  160 (213)
T cd03752          81 ANILINYARLIAQRYLYSYQEPIPVEQLVQRLCDIKQGYTQYGGLRPFGVSFLYAGWDKHYGFQLYQSDPSGNYSGWKAT  160 (213)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCcccceeEEEEEEEeCCCCCEEEEECCCCCeeeeeEE
Confidence            99999999999999999999999999999999999999999999999999999999997668999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          163 AIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      |+|+++.+++++||+.|+++|+++||++++++||+.+.+|+...+.+++|++|
T Consensus       161 a~G~gs~~~~~~Le~~y~~~ms~eea~~l~~~al~~~~~r~~~~~~~~ei~~~  213 (213)
T cd03752         161 AIGNNNQAAQSLLKQDYKDDMTLEEALALAVKVLSKTMDSTKLTSEKLEFATL  213 (213)
T ss_pred             EECCCcHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEC
Confidence            99999999999999999999999999999999999999999999999999875

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>KOG0178 consensus 20S proteasome, regulatory subunit alpha type PSMA4/PRE9 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.9e-59  Score=371.99  Aligned_cols=247  Identities=66%  Similarity=0.996  Sum_probs=238.2

Q ss_pred             CCCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         1 ~~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      |||+||...|+|||||||+|||||++++++.+|+|||..+||||||++++.+++++..+...+||++|+|+|+|+++|+.
T Consensus         1 msr~ydsrttiFspEGRLyQVEyAmeais~aGt~iGila~DGvvLa~e~k~t~kll~t~~~~EKiY~l~d~iaC~vaGlt   80 (249)
T KOG0178|consen    1 MSRRYDSRTTIFSPEGRLYQVEYAMEAISHAGTCIGILASDGVVLAGENKVTSKLLDTSIPMEKIYKLNDNIACAVAGLT   80 (249)
T ss_pred             CCcCcCCcccccCCCcchHHHHHHHHHHhhhcceeEEEecCceEEEeecccchhhhhccccHHHhhhcCCceEEEEeccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce
Q 025640           81 SDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK  160 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~  160 (250)
                      +|+..|++.+|..++.|.+.|++++|.+.|++.+++..|.|||+.|.|||||++|.+|||+..|.+||+.||+|++..|+
T Consensus        81 ~DAnvL~n~aRi~AQ~yl~~y~e~iP~eqLv~~lcdiKQayTQygG~RPFGVSfLYaGwd~~~gyqLy~SdPSGny~gWk  160 (249)
T KOG0178|consen   81 SDANVLKNYARIIAQRYLFRYGEEIPCEQLVTFLCDIKQAYTQYGGKRPFGVSFLYAGWDDRYGYQLYQSDPSGNYGGWK  160 (249)
T ss_pred             ccHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHhhccCcCCCceeeeeeceecCcceEEEecCCCCCccccc
Confidence            99999999999999999999999999999999999999999999999999999999999998899999999999999999


Q ss_pred             EEEEeCChHHHHHHHHhhCCCCC-CHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          161 AAAIGANNQAAQSILKQDYKDDI-SREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       161 ~~a~G~g~~~~~~~L~~~~~~~~-s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      +.|+|.++..+++.|...|+++. +++||+.+|++.|..+.++...+...+|++.++++.+.. .+++++++||..++++
T Consensus       161 a~ciG~N~~Aa~s~Lkqdykdd~~~~~eA~~laikvL~kt~d~~~lt~eklEia~~~k~~~k~-v~~i~~~~ev~kll~k  239 (249)
T KOG0178|consen  161 ATCIGANSGAAQSMLKQDYKDDENDLEEAKALAIKVLSKTLDSGSLTAEKLEIATITKDCNKT-VLKILKKDEVLKLLEK  239 (249)
T ss_pred             eeeeccchHHHHHHHHhhhccccccHHHHHHHHHHHHHhhcccCCCChhheEEEEEEecCCce-EEEecCHHHHHHHHHH
Confidence            99999999999999999999765 599999999999999999999999999999999998654 5899999999999999


Q ss_pred             hCCCCcccc
Q 025640          240 HGVTQPAAE  248 (250)
Q Consensus       240 ~~~~~~~~~  248 (250)
                      +.+.+.+++
T Consensus       240 ~~~~~~~~~  248 (249)
T KOG0178|consen  240 YHETQRQAE  248 (249)
T ss_pred             hhhhhhhcc
Confidence            998876654

>TIGR03633 arc_protsome_A proteasome endopeptidase complex, archaeal, alpha subunit

Probab=100.00  E-value=2.9e-58  Score=387.23  Aligned_cols=223  Identities=47%  Similarity=0.779  Sum_probs=211.8

Q ss_pred             CCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHH
Q 025640            4 RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDA   83 (250)
Q Consensus         4 ~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~   83 (250)
                      +||+++|+|||||||+|||||++|+.+|+|+|||+++||||||+|+|.++++ ...++.+||++|+++++|++||..+|+
T Consensus         2 ~~~~~~~~f~p~Grl~Qieya~~av~~G~tvigi~~~dgvvlaad~r~~~~~-~~~~~~~KI~~i~~~i~~~~sG~~~D~   80 (224)
T TIGR03633         2 GYDRAITVFSPDGRLYQVEYAREAVKRGTTAVGIKTKDGVVLAVDKRITSKL-VEPSSIEKIFKIDDHIGAATSGLVADA   80 (224)
T ss_pred             CCCCCCceECCCCeEeHHHHHHHHHHcCCCEEEEEECCEEEEEEeccCCccc-cCCCccceEEEECCCEEEEEeecHHhH
Confidence            6999999999999999999999999999999999999999999999998654 444688999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEE
Q 025640           84 NILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAA  163 (250)
Q Consensus        84 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a  163 (250)
                      +.+.+.++.++..|++.++.+++++.+++.|++.+|.|+++++.|||+|++||||+|+ ++|+||.+||.|++.+++++|
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~ls~~l~~~~~~~~~rP~~v~~ll~G~d~-~~~~Ly~~D~~G~~~~~~~~a  159 (224)
T TIGR03633        81 RVLIDRARIEAQINRLTYGEPIDVETLAKKICDLKQQYTQHGGVRPFGVALLIAGVDD-GGPRLFETDPSGALLEYKATA  159 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCccccceEEEEEEEeC-CcCEEEEECCCCCeecceEEE
Confidence            9999999999999999999999999999999999999999999999999999999996 589999999999999999999


Q ss_pred             EeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHH
Q 025640          164 IGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEA  232 (250)
Q Consensus       164 ~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~e  232 (250)
                      +|.++.+++++|++.|+++|+++||++++++||+.+.+ ++.+++.++|++|++++.   .|+.++++|
T Consensus       160 ~G~g~~~~~~~L~~~~~~~~~~eeai~l~~~al~~~~~-d~~~~~~i~i~ii~~~g~---~~~~~~~~~  224 (224)
T TIGR03633       160 IGAGRQAVTEFLEKEYREDLSLDEAIELALKALYSAVE-DKLTPENVEVAYITVEDK---KFRKLSVEE  224 (224)
T ss_pred             ECCCCHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHhc-ccCCCCcEEEEEEEcCCC---cEEECCCCC
Confidence            99999999999999999999999999999999999998 889999999999999873   378888764

This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated.

>cd03751 proteasome_alpha_type_3 proteasome_alpha_type_3

Probab=100.00  E-value=6.4e-58  Score=381.50  Aligned_cols=211  Identities=41%  Similarity=0.644  Sum_probs=202.0

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      ++||+++|+|||||||+|||||++|+++|+|+|||+++||||||+|++.++.+... ++.+||++|+++++|+++|..+|
T Consensus         2 ~~yd~~~t~fsp~Grl~Qveya~~a~~~G~tvIgik~kdgVvla~d~r~~~~~~~~-~~~~KI~~I~~~i~~~~sG~~~D   80 (212)
T cd03751           2 TGYDLSASTFSPDGRVFQVEYANKAVENSGTAIGIRCKDGVVLAVEKLVTSKLYEP-GSNKRIFNVDRHIGIAVAGLLAD   80 (212)
T ss_pred             CCccCCCceECCCCcchHHHHHHHHHhcCCCEEEEEeCCEEEEEEEccccccccCc-chhcceeEecCcEEEEEEEChHh
Confidence            58999999999999999999999999999999999999999999999998766654 47899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+.+|.++..|++.++.+++++.+++.|++.+|.|+++++.|||+|++||+|||+. ||+||.+||+|++.+++++
T Consensus        81 ~~~l~~~~r~~~~~y~~~~~~~~~v~~la~~ls~~~~~~t~~~~~rP~~vs~li~G~D~~-gp~Ly~~D~~Gs~~~~~~~  159 (212)
T cd03751          81 GRHLVSRAREEAENYRDNYGTPIPVKVLADRVAMYMHAYTLYSSVRPFGCSVLLGGYDSD-GPQLYMIEPSGVSYGYFGC  159 (212)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccCCCcCCceEEEEEEEEeCC-cCEEEEECCCCCEEeeEEE
Confidence            999999999999999999999999999999999999999999999999999999999974 8999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          163 AIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      |+|+|+.+++++||+.|+++||++||+++++++|+.+.+.......+|||+++
T Consensus       160 a~G~g~~~a~~~Lek~~~~dms~eeai~l~~~~L~~~~~~~~~~~~~iei~~~  212 (212)
T cd03751         160 AIGKGKQAAKTELEKLKFSELTCREAVKEAAKIIYIVHDEIKDKAFELELSWV  212 (212)
T ss_pred             EECCCCHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHhhccCCCCccEEEEEC
Confidence            99999999999999999999999999999999999999877788899999874

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>KOG0176 consensus 20S proteasome, regulatory subunit alpha type PSMA5/PUP2 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.2e-58  Score=361.71  Aligned_cols=229  Identities=42%  Similarity=0.711  Sum_probs=217.5

Q ss_pred             CCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHH
Q 025640            4 RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDA   83 (250)
Q Consensus         4 ~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~   83 (250)
                      .||+.+++|||||||||||||.+|++.|+|.|||+.++|||||+++|.++.++.++ +..||++|++||+|++||+.+|+
T Consensus         7 eydrgVNTfSpEGRlfQVEYaieAikLGsTaIGv~TkEgVvL~vEKritSpLm~p~-sveKi~eid~HIgca~SGl~aDa   85 (241)
T KOG0176|consen    7 EYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGVKTKEGVVLAVEKRITSPLMEPS-SVEKIVEIDDHIGCAMSGLIADA   85 (241)
T ss_pred             HhcccccccCCCceeeehhhHHHHHhcCCceeeeeccceEEEEEeccccCcccCch-hhhhheehhhceeeeccccccch
Confidence            79999999999999999999999999999999999999999999999999999987 78999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhcccc-----CCCcceeEEEEEEEEeCCCCeEEEEECCCCceec
Q 025640           84 NILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF-----GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGG  158 (250)
Q Consensus        84 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~-----~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~  158 (250)
                      +.+++.+|.++++|.+.||++++++.+.+.+|++...|...     .-.|||||++|+||+|+ .||+||+.||+|+|..
T Consensus        86 rTlve~arv~~qnh~f~Y~e~i~VEs~tq~v~~LaLrFGe~~~~~~~msRPFGValliAG~D~-~gpqL~h~dPSGtf~~  164 (241)
T KOG0176|consen   86 RTLVERARVETQNHWFTYGEPISVESLTQAVSDLALRFGEGDDEEAIMSRPFGVALLIAGHDE-TGPQLYHLDPSGTFIR  164 (241)
T ss_pred             HHHHHHHHHHhhhceeecCCcccHHHHHHHHHHHHhHhCCCcchhhhhcCCcceEEEEeeccC-CCceEEEeCCCCceEE
Confidence            99999999999999999999999999999999987666543     23599999999999997 5999999999999999


Q ss_pred             ceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 025640          159 WKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLV  238 (250)
Q Consensus       159 ~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~  238 (250)
                      |++-|||+|++.+++.|++.|.++|+++||+.+++..|+.+++ +..+.+++++.+|++++    .|++++++|++.++.
T Consensus       165 ~~AKAIGSgsEga~~~L~~e~~~~ltL~ea~~~~L~iLkqVMe-eKl~~~Nvev~~vt~e~----~f~~~t~EE~~~~i~  239 (241)
T KOG0176|consen  165 YKAKAIGSGSEGAESSLQEEYHKDLTLKEAEKIVLKILKQVME-EKLNSNNVEVAVVTPEG----EFHIYTPEEVEQVIK  239 (241)
T ss_pred             ecceeccccchHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHH-HhcCccceEEEEEcccC----ceEecCHHHHHHHHh
Confidence            9999999999999999999999999999999999999999998 78899999999999986    489999999999876


Q ss_pred             H
Q 025640          239 K  239 (250)
Q Consensus       239 ~  239 (250)
                      +
T Consensus       240 ~  240 (241)
T KOG0176|consen  240 R  240 (241)
T ss_pred             c
Confidence            5

>cd03755 proteasome_alpha_type_7 proteasome_alpha_type_7

Probab=100.00  E-value=3.1e-57  Score=376.63  Aligned_cols=207  Identities=42%  Similarity=0.725  Sum_probs=198.2

Q ss_pred             CCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHH
Q 025640            5 YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDAN   84 (250)
Q Consensus         5 yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~   84 (250)
                      ||+++|+|||||||+|||||++|+++|+|+|||+++||||||+|++.+..+.. ++..+||++|+++++|++||+.+|++
T Consensus         1 ~d~~~~~fsp~Gr~~Qveya~~av~~G~t~Igik~~dgVvlaad~~~~~~~~~-~~~~~KI~~I~~~i~~~~sG~~~D~~   79 (207)
T cd03755           1 YDRAITVFSPDGHLFQVEYAQEAVRKGTTAVGVRGKDCVVLGVEKKSVAKLQD-PRTVRKICMLDDHVCLAFAGLTADAR   79 (207)
T ss_pred             CCCCCceECCCCeEeHHHHHHHHHHcCCCEEEEEeCCEEEEEEecCCCCcccC-CCccCcEEEECCCEEEEEecchhhHH
Confidence            89999999999999999999999999999999999999999999998776544 45789999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEE
Q 025640           85 ILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAI  164 (250)
Q Consensus        85 ~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~  164 (250)
                      .+.+.++.++..|++.++++++++.+++.++..+|.|+++++.|||+|++||+|||++++|+||.+||+|++.+++++|+
T Consensus        80 ~l~~~~r~~~~~~~~~~~~~i~~~~la~~ls~~~~~y~~~~~~rP~~vs~ii~G~D~~~~p~Ly~iD~~G~~~~~~~~a~  159 (207)
T cd03755          80 VLINRARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQSGGVRPFGISTLIVGFDPDGTPRLYQTDPSGTYSAWKANAI  159 (207)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCcccceeEEEEEEEeCCCCeEEEEECCCcCEEcceEEEE
Confidence            99999999999999999999999999999999999999999999999999999999867899999999999999999999


Q ss_pred             eCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          165 GANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       165 G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      |.|+.+++++||+.|+++|+++||++++++||+.+.+   .++.++||+++
T Consensus       160 G~gs~~~~~~Le~~~~~~ms~eeai~l~~~~l~~~~~---~~~~~~e~~~~  207 (207)
T cd03755         160 GRNSKTVREFLEKNYKEEMTRDDTIKLAIKALLEVVQ---SGSKNIELAVM  207 (207)
T ss_pred             CCCCHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhC---CCCCeEEEEEC
Confidence            9999999999999999999999999999999999997   68889999875

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03749 proteasome_alpha_type_1 proteasome_alpha_type_1

Probab=100.00  E-value=7.9e-57  Score=375.03  Aligned_cols=208  Identities=40%  Similarity=0.682  Sum_probs=199.4

Q ss_pred             CCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHH
Q 025640            5 YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDAN   84 (250)
Q Consensus         5 yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~   84 (250)
                      ||+++|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.++++.   ++.+||++|+++++|++||+.+|++
T Consensus         1 yd~~~t~fsp~Grl~Qveya~~av~~G~t~IgIk~~dgVvlaad~r~~~~l~---~~~~KI~~I~~~i~~~~sG~~~D~~   77 (211)
T cd03749           1 YDTDVTTWSPQGRLFQVEYAMEAVKQGSATVGLKSKTHAVLVALKRATSELS---SYQKKIFKVDDHIGIAIAGLTADAR   77 (211)
T ss_pred             CCCCCceECCCCeEeHHHHHHHHHhcCCCEEEEEeCCEEEEEEeccCccccC---CccccEEEeCCCEEEEEEeChHhHH
Confidence            8999999999999999999999999999999999999999999999887742   3669999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEE
Q 025640           85 ILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAI  164 (250)
Q Consensus        85 ~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~  164 (250)
                      .+.+.++.++..|++.++++++++.+++.++..+|.++++.+.|||+|++||+|||+. ||+||++||+|++.+++++|+
T Consensus        78 ~l~~~~r~~~~~~~~~~~~~~~v~~la~~is~~~~~~t~~~~~rP~~v~~ii~G~D~~-gp~Ly~~Dp~G~~~~~~~~a~  156 (211)
T cd03749          78 VLSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQRYGRRPYGVGLLIAGYDES-GPHLFQTCPSGNYFEYKATSI  156 (211)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCCCCceEEEEEEEEcCC-CCeEEEECCCcCEeeeeEEEE
Confidence            9999999999999999999999999999999999999999999999999999999974 899999999999999999999


Q ss_pred             eCChHHHHHHHHhhCC--CCCCHHHHHHHHHHHHHHhhcCCC-CCCCcEEEEEEE
Q 025640          165 GANNQAAQSILKQDYK--DDISREEAVQLALKVLSKTMDSTS-LTSDKLELAEVF  216 (250)
Q Consensus       165 G~g~~~~~~~L~~~~~--~~~s~~ea~~l~~~~l~~~~~~~~-~~~~~iei~ii~  216 (250)
                      |.++.+++++||++|+  ++|+++||+++++++|+.+.+++. .++.+|||++|+
T Consensus       157 G~g~~~a~~~Le~~~~~~~~ms~ee~i~~~~~~l~~~~~~~~~~~~~~iei~ii~  211 (211)
T cd03749         157 GARSQSARTYLERHFEEFEDCSLEELIKHALRALRETLPGEQELTIKNVSIAIVG  211 (211)
T ss_pred             CCCcHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhccCCCCCCCcEEEEEEC
Confidence            9999999999999998  699999999999999999998877 999999999983

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>COG0638 PRE1 20S proteasome, alpha and beta subunits [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.2e-56  Score=376.30  Aligned_cols=234  Identities=44%  Similarity=0.692  Sum_probs=224.0

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCC-ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNA-GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMS   81 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g-~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~   81 (250)
                      .+||+.+++|+|+|+++|+|||.+++.+| +|+|||+++||||||+|+|.++++++.+++.+|||+|+|||+|+++|+.+
T Consensus         1 ~~~~~~~~~fsp~g~l~q~e~a~~a~~~~gtT~vgik~~dgVVlaadkr~t~~~~~~~~~~~Ki~~I~d~i~~~~sG~~a   80 (236)
T COG0638           1 AGYDRAITIFSPEGRLFQVEYALEAVKRGGTTTVGIKGKDGVVLAADKRATSGLLIASSNVEKIFKIDDHIGMAIAGLAA   80 (236)
T ss_pred             CCCcCcceeECCCCchHHHHHHHHHHHcCCceEEEEEecCEEEEEEeccCCCCceecccccceEEEecCCEEEEeccCcH
Confidence            37999999999999999999999999987 99999999999999999999999999998899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceE
Q 025640           82 DANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKA  161 (250)
Q Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~  161 (250)
                      |++.+++.++.++..|++.++++++++.+++.+++.+|.++++  .|||++++||||+|+ ++|+||++||+|++.++++
T Consensus        81 Da~~lv~~~r~~a~~~~~~~~~~i~v~~la~~ls~~l~~~~~~--~rP~gv~~iiaG~d~-~~p~Ly~~Dp~G~~~~~~~  157 (236)
T COG0638          81 DAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQS--GRPYGVSLLVAGVDD-GGPRLYSTDPSGSYNEYKA  157 (236)
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccC--cccceEEEEEEEEcC-CCCeEEEECCCCceeecCE
Confidence            9999999999999999999999999999999999999999987  899999999999999 7899999999999999999


Q ss_pred             EEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhC
Q 025640          162 AAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHG  241 (250)
Q Consensus       162 ~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~  241 (250)
                      +|+|+|+.+++++||+.|+++|++|||++++++||+.+++|+..++++++|++++++.    .++.++.++++.++..+.
T Consensus       158 ~a~Gsgs~~a~~~Le~~y~~~m~~eeai~la~~al~~a~~rd~~s~~~~~v~vi~~~~----~~~~~~~~~~~~~~~~~~  233 (236)
T COG0638         158 TAIGSGSQFAYGFLEKEYREDLSLEEAIELAVKALRAAIERDAASGGGIEVAVITKDE----GFRKLDGEEIKKLLDDLS  233 (236)
T ss_pred             EEEcCCcHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHhccccCCCCeEEEEEEcCC----CeEEcCHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999999999899999999999853    289999999999988766


Q ss_pred             CC
Q 025640          242 VT  243 (250)
Q Consensus       242 ~~  243 (250)
                      +.
T Consensus       234 ~~  235 (236)
T COG0638         234 EK  235 (236)
T ss_pred             hc
Confidence            43

>cd03756 proteasome_alpha_archeal proteasome_alpha_archeal

Probab=100.00  E-value=1.7e-56  Score=373.19  Aligned_cols=210  Identities=51%  Similarity=0.831  Sum_probs=201.0

Q ss_pred             CCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHH
Q 025640            4 RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDA   83 (250)
Q Consensus         4 ~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~   83 (250)
                      +||+++|+|||||||+|+|||.||+++|+|+|||+++||||||+|++.+.++.. .++.+||++|+++++|++||..+|+
T Consensus         1 ~y~~~~~~fsp~G~l~Q~eya~~av~~G~t~igik~~dgvvla~d~~~~~~~~~-~~~~~KI~~I~~~i~~~~sG~~~D~   79 (211)
T cd03756           1 GYDRAITVFSPDGRLYQVEYAREAVKRGTTALGIKCKEGVVLAVDKRITSKLVE-PESIEKIYKIDDHVGAATSGLVADA   79 (211)
T ss_pred             CCCCCCceECCCCeEhHHHHHHHHHHcCCCEEEEEECCEEEEEEeccCCCcccC-CCccceEEEEcCCEEEEEecCHHHH
Confidence            699999999999999999999999999999999999999999999999865544 5688999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEE
Q 025640           84 NILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAA  163 (250)
Q Consensus        84 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a  163 (250)
                      +.+.+.++.++..|++.++.+++++.+++.|+..++.++++++.|||++++||+|||+ .+|+||.+||.|++.++++++
T Consensus        80 ~~l~~~l~~~~~~~~~~~~~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~~ll~G~D~-~~~~ly~vd~~G~~~~~~~~a  158 (211)
T cd03756          80 RVLIDRARVEAQIHRLTYGEPIDVEVLVKKICDLKQQYTQHGGVRPFGVALLIAGVDD-GGPRLFETDPSGAYNEYKATA  158 (211)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCeechhEEEEEEEEeC-CCCEEEEECCCCCeeeeEEEE
Confidence            9999999999999999999999999999999999999999999999999999999997 489999999999999999999


Q ss_pred             EeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEE
Q 025640          164 IGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVF  216 (250)
Q Consensus       164 ~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~  216 (250)
                      +|+++++++++|++.|+++|+++||++++++||+.+.+++ ..+++++|++|+
T Consensus       159 ~G~g~~~~~~~Le~~~~~~m~~~ea~~l~~~~l~~~~~~~-~~~~~~~v~ii~  210 (211)
T cd03756         159 IGSGRQAVTEFLEKEYKEDMSLEEAIELALKALYAALEEN-ETPENVEIAYVT  210 (211)
T ss_pred             ECCCCHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhccc-CCCCcEEEEEEe
Confidence            9999999999999999999999999999999999998865 599999999986

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03754 proteasome_alpha_type_6 proteasome_alpha_type_6

Probab=100.00  E-value=1.7e-56  Score=374.00  Aligned_cols=210  Identities=38%  Similarity=0.685  Sum_probs=199.4

Q ss_pred             CCCCCccccCCCCcccccchHHHHhcC-CccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            4 RYDSRTTIFSPEGRLYQVEYAMEAIGN-AGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         4 ~yd~~~~~f~p~G~l~qveya~~a~~~-g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      +||+++|+|||||||+|||||++|+++ |+|+|||+++||||||+|+|.+.++...+ +.+||++|+++++|++||+.+|
T Consensus         1 ~yd~~~~~fsp~Grl~Qveya~~a~~~~g~t~igi~~~d~Vvlaad~r~~~~~i~~~-~~~Ki~~I~~~i~~~~sG~~~D   79 (215)
T cd03754           1 GFDRHITIFSPEGRLYQVEYAFKAVKNAGLTSVAVRGKDCAVVVTQKKVPDKLIDPS-TVTHLFRITDEIGCVMTGMIAD   79 (215)
T ss_pred             CCCCCCeeECCCCeEeHHHhHHHHHhcCCccEEEEEeCCEEEEEEeccccccccCCc-ccCceEEEcCCEEEEEEechhh
Confidence            699999999999999999999999975 77999999999999999999988776654 7889999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+++|.++..|++.++++++++.+|+.+++++|.|+++++.|||++++||+|||++.||+||.+||+|++.+++++
T Consensus        80 ~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~q~yt~~~~~RP~~v~~ii~G~D~~~gp~Ly~~Dp~Gs~~~~~~~  159 (215)
T cd03754          80 SRSQVQRARYEAAEFKYKYGYEMPVDVLAKRIADINQVYTQHAYMRPLGVSMILIGIDEELGPQLYKCDPAGYFAGYKAT  159 (215)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhCCCCCcCCeeEEEEEEEeCCCCeEEEEEcCCccEEeEEEE
Confidence            99999999999999999999999999999999999999999999999999999999997668999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhCCCC--C--CHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          163 AIGANNQAAQSILKQDYKDD--I--SREEAVQLALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~~~~--~--s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      |+|.|+.+++++||+.|+++  |  |.+||++++++||..+.+|+. .++.+||++|
T Consensus       160 a~G~gs~~~~~~Le~~~~~~~~~~~s~eeai~l~~~al~~~~~rd~-~~~~~ei~~~  215 (215)
T cd03754         160 AAGVKEQEATNFLEKKLKKKPDLIESYEETVELAISCLQTVLSTDF-KATEIEVGVV  215 (215)
T ss_pred             EECCCcHHHHHHHHHHhccccccCCCHHHHHHHHHHHHHHHhcccC-CCCcEEEEEC
Confidence            99999999999999999985  7  999999999999999998774 5999999875

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd01911 proteasome_alpha proteasome alpha subunit

Probab=100.00  E-value=4.3e-56  Score=370.37  Aligned_cols=209  Identities=56%  Similarity=0.929  Sum_probs=201.8

Q ss_pred             CCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHH
Q 025640            5 YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDAN   84 (250)
Q Consensus         5 yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~   84 (250)
                      ||+++|+|||||||+|+|||.+++.+|+|+|||+++||||||+|++.+.++. ..++.+||++|+++++|+++|..+|++
T Consensus         1 ~~~~~~~f~~~G~~~q~eya~~~~~~G~tvigi~~~dgVvlaaD~~~~~~~~-~~~~~~KI~~i~~~i~~~~sG~~~D~~   79 (209)
T cd01911           1 YDRSITTFSPEGRLFQVEYALEAVKNGSTAVGIKGKDGVVLAVEKKVTSKLL-DPSSVEKIFKIDDHIGCAVAGLTADAR   79 (209)
T ss_pred             CCCCCccCCCCCEEeHHHHHHHHHHcCCCEEEEEECCEEEEEEEecCCcccc-CCcccceEEEecCCeEEEeccCcHhHH
Confidence            8999999999999999999999999999999999999999999999998755 446889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEE
Q 025640           85 ILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAI  164 (250)
Q Consensus        85 ~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~  164 (250)
                      .+.+.++..+..|++.++.+++++.+++.+++.++.|+++++.||++|++||+|||++.+|+||.+||.|++.+++++++
T Consensus        80 ~l~~~l~~~~~~~~~~~g~~~~~~~la~~ls~~~~~~~~~~~~rP~~v~~iv~G~d~~~~~~Ly~iD~~G~~~~~~~~a~  159 (209)
T cd01911          80 VLVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQYGGVRPFGVSLLIAGYDEEGGPQLYQTDPSGTYFGYKATAI  159 (209)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccChhheEEEEEEcCCCCcEEEEECCCCCeeeeeEEEe
Confidence            99999999999999999999999999999999999999999999999999999999877899999999999999999999


Q ss_pred             eCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          165 GANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       165 G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      |.++.+++++|++.|+++|+++||++++.+||+.+.+|+. +++.++|+++
T Consensus       160 G~g~~~~~~~L~~~~~~~ms~~ea~~l~~~~l~~~~~~d~-~~~~~~i~i~  209 (209)
T cd01911         160 GKGSQEAKTFLEKRYKKDLTLEEAIKLALKALKEVLEEDK-KAKNIEIAVV  209 (209)
T ss_pred             CCCcHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHhccC-CCCcEEEEEC
Confidence            9999999999999999999999999999999999999998 9999999875

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 different alpha and 10 different beta proteasome subunit genes while archaea have one of each.

>KOG0184 consensus 20S proteasome, regulatory subunit alpha type PSMA3/PRE10 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.2e-55  Score=352.97  Aligned_cols=243  Identities=37%  Similarity=0.573  Sum_probs=226.8

Q ss_pred             CC---CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEe
Q 025640            1 MS---RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVA   77 (250)
Q Consensus         1 ~~---~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~s   77 (250)
                      ||   .+||++.++||||||+||||||.||+.||+|||||+|+|||||++++..+++++.+. ...||+.|++||+|+++
T Consensus         1 MSsIGtGyDls~s~fSpdGrvfQveYA~KAven~~T~IGIk~kdGVVl~vEKli~SkLy~p~-sn~ri~~V~r~iG~ava   79 (254)
T KOG0184|consen    1 MSSIGTGYDLSASTFSPDGRVFQVEYAQKAVENSGTCIGIKCKDGVVLAVEKLITSKLYEPG-SNERIFSVDRHIGMAVA   79 (254)
T ss_pred             CCcccccccccceeeCCCCceehHHHHHHHHhcCCcEEEEecCCeEEEEEeeeecccccccC-CCCceEeecccccEEEe
Confidence            88   799999999999999999999999999999999999999999999999999999987 56899999999999999


Q ss_pred             CchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCcee
Q 025640           78 GIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYG  157 (250)
Q Consensus        78 G~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~  157 (250)
                      |+.+|.+.+...+|.++..|+.+|+.++|...++..++++.|.||.++..|||||+.++++||+ .||+||+++|+|.++
T Consensus        80 Gl~~Dg~~l~~~ar~ea~~~~~~y~~piP~~~la~rva~yvh~~Tly~~vRpfG~~~~~~~yd~-~g~~LymiepSG~~~  158 (254)
T KOG0184|consen   80 GLIPDGRHLVNRARDEAASWRKNYGDPIPGKHLADRVADYVHAFTLYSSVRPFGASTILGSYDD-EGPQLYMIEPSGSSY  158 (254)
T ss_pred             ccccchHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHhhhheeehhhccccccceEEEEEEeC-CCceEEEEcCCCCcc
Confidence            9999999999999999999999999999999999999999999999999999999999999996 599999999999999


Q ss_pred             cceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 025640          158 GWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL  237 (250)
Q Consensus       158 ~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~  237 (250)
                      .++++|+|.|.+.+++.||+.--.+|+.+|+++-+-+.+..+.+........+||.++..+.++   .+..-|.||.+..
T Consensus       159 ~Y~~aaiGKgrq~aKtElEKL~~~~mt~~e~VkeaakIiY~~HDe~KdK~feiEm~wvg~eTnG---~h~~vp~el~~ea  235 (254)
T KOG0184|consen  159 GYKGAAIGKGRQAAKTELEKLKIDEMTCKELVKEAAKIIYKVHDENKDKEFEIEMGWVGEETNG---LHEKVPSELLEEA  235 (254)
T ss_pred             ceeeeeccchhHHHHHHHHhcccccccHHHHHHHHHheeEeecccccCcceEEEEEEEEeecCC---ccccCcHHHHHHH
Confidence            9999999999999999999998899999999999999999999998999999999999987765   3555556888777


Q ss_pred             HHhCCCCcccc
Q 025640          238 VKHGVTQPAAE  248 (250)
Q Consensus       238 ~~~~~~~~~~~  248 (250)
                      .++.+...+|.
T Consensus       236 ~~~a~~s~~~~  246 (254)
T KOG0184|consen  236 EKYAKASLDEE  246 (254)
T ss_pred             HHHHHhhhccc
Confidence            77665544443

>cd03753 proteasome_alpha_type_5 proteasome_alpha_type_5

Probab=100.00  E-value=1e-54  Score=362.97  Aligned_cols=208  Identities=47%  Similarity=0.764  Sum_probs=196.5

Q ss_pred             CCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHH
Q 025640            5 YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDAN   84 (250)
Q Consensus         5 yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~   84 (250)
                      ||+++|+|||||||+|||||++|+++|+|+|||+++||||||+|++.++++.. .++.+||++|+++++|+++|+.+|++
T Consensus         1 ~~~~~~~f~p~G~~~Q~eya~~a~~~G~t~igik~~dgVvlaad~r~~~~~~~-~~~~~KI~~I~~~i~~~~sG~~~D~~   79 (213)
T cd03753           1 YDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIKTKEGVVLAVEKRITSPLME-PSSVEKIMEIDDHIGCAMSGLIADAR   79 (213)
T ss_pred             CCCCCccCCCCCeEhHHHHHHHHHhcCCCEEEEEeCCEEEEEEecccCCcCcC-CCccceEEEEcCCEEEEEecCHHHHH
Confidence            89999999999999999999999999999999999999999999999877654 45789999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccC-----CCcceeEEEEEEEEeCCCCeEEEEECCCCceecc
Q 025640           85 ILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFG-----GLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW  159 (250)
Q Consensus        85 ~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~-----~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~  159 (250)
                      .+.+.++.++..|++.++++++++.+++.|+..++.|+++.     ..|||+|++||+|||+ .||+||.+||.|++.++
T Consensus        80 ~l~~~~r~~~~~~~~~~~~~i~~~~~~~~ls~~~~~~~~~~~~~~~~~rP~~v~~ii~G~D~-~gp~Ly~vd~~G~~~~~  158 (213)
T cd03753          80 TLIDHARVEAQNHRFTYNEPMTVESVTQAVSDLALQFGEGDDGKKAMSRPFGVALLIAGVDE-NGPQLFHTDPSGTFTRC  158 (213)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhCcccccccccccceEEEEEEEEcC-CCCEEEEECCCCCeecc
Confidence            99999999999999999999999999999999999888743     4699999999999997 48999999999999999


Q ss_pred             eEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          160 KAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       160 ~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      +++|+|.++++++++|+++|+++|+++||++++++||+.+.++ ..++.+++|++|
T Consensus       159 ~~~a~G~~~~~~~~~L~~~~~~~ls~eeai~l~~~~l~~~~~~-~~~~~~~ei~~~  213 (213)
T cd03753         159 DAKAIGSGSEGAQSSLQEKYHKDMTLEEAEKLALSILKQVMEE-KLNSTNVELATV  213 (213)
T ss_pred             cEEEECCCcHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhcc-cCCCCcEEEEEC
Confidence            9999999999999999999999999999999999999998874 588899999975

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=5.1e-55  Score=347.54  Aligned_cols=234  Identities=35%  Similarity=0.600  Sum_probs=221.7

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      .+||+.+|+|||||+|||||||++|+.+|+++||++++++|||+.+++....+... +...||..+++|++|+++|+.+|
T Consensus         2 srydraltvFSPDGhL~QVEYAqEAvrkGstaVgvrg~~~vvlgvEkkSv~~Lq~~-r~~rkI~~ld~hV~mafaGl~aD   80 (249)
T KOG0183|consen    2 SRYDRALTVFSPDGHLFQVEYAQEAVRKGSTAVGVRGNNCVVLGVEKKSVPKLQDE-RTVRKISMLDDHVVMAFAGLTAD   80 (249)
T ss_pred             CccccceEEECCCCCEEeeHhHHHHHhcCceEEEeccCceEEEEEeecchhhhhhh-hhhhhheeecceeeEEecCCCcc
Confidence            47999999999999999999999999999999999999999999999988777774 46899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+++.+|-+|+.|+++...+++++.+.++|+.+.|.|||..+.||||+++||+|+|+++.|.||.+||+|.|.+|++-
T Consensus        81 ArilinrArvecqShrlt~edpvtveyitRyiA~~kQrYTqs~grRPFGvs~Li~GfD~~g~p~lyqtePsG~f~ewka~  160 (249)
T KOG0183|consen   81 ARILINRARVECQSHRLTLEDPVTVEYITRYIAGLKQRYTQSNGRRPFGVSTLIGGFDPDGTPRLYQTEPSGIFSEWKAN  160 (249)
T ss_pred             ceeehhhHhHhhhhhhcccCCCcHHHHHHHHHHHhhhhhhccCCcccccceEEEEeeCCCCCeeeEeeCCCcchhhhhcc
Confidence            99999999999999999999999999999999999999999999999999999999999888999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhCCCC--CCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 025640          163 AIGANNQAAQSILKQDYKDD--ISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH  240 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~~~~--~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~  240 (250)
                      |+|.++..+..+||++|.+.  .+..++++|+.++|..+..   ..+.+|+++++.+.+    .++.++.++|+.++..+
T Consensus       161 aiGr~sk~VrEflEK~y~e~~~~~~~~~ikL~ir~LleVvq---s~~~nie~aVm~~~~----~~~~l~~~~I~~~v~~i  233 (249)
T KOG0183|consen  161 AIGRSSKTVREFLEKNYKEEAIATEGETIKLAIRALLEVVQ---SGGKNIEVAVMKRRK----DLKMLESEEIDDIVKEI  233 (249)
T ss_pred             ccccccHHHHHHHHHhcccccccccccHHHHHHHHHHHHhh---cCCCeeEEEEEecCC----ceeecCHHHHHHHHHHH
Confidence            99999999999999999866  7889999999999999986   457899999999876    38999999999999998


Q ss_pred             CCCC
Q 025640          241 GVTQ  244 (250)
Q Consensus       241 ~~~~  244 (250)
                      +...
T Consensus       234 e~E~  237 (249)
T KOG0183|consen  234 EQEE  237 (249)
T ss_pred             HHHH
Confidence            8763

>KOG0181 consensus 20S proteasome, regulatory subunit alpha type PSMA2/PRE8 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.6e-53  Score=332.49  Aligned_cols=232  Identities=37%  Similarity=0.647  Sum_probs=221.0

Q ss_pred             CCCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         1 ~~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      |..+|..++|+|||+|+|-|+|||+.|+.+|.+.|||+-.||||||++++..+.+.+. .+..|++.|.++|+|.+||+.
T Consensus         2 ~d~~y~fslTtFSpsGKL~QieyAL~Av~~G~~SvGi~A~nGvVlatekk~~s~L~~~-~sv~KV~~i~~~IG~vYSGmg   80 (233)
T KOG0181|consen    2 GDFGYSFSLTTFSPSGKLVQIEYALTAVVNGQTSVGIKAANGVVLATEKKDVSPLVDE-ESVRKVEKITPHIGCVYSGMG   80 (233)
T ss_pred             CCcccceeeEEEcCCCceehHHHHHHHHhCCCCceeeeecCceEEEeccCCCCccchh-hhhhhHhhccCCcceEEecCC
Confidence            3459999999999999999999999999999999999999999999999888888775 478999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce
Q 025640           81 SDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK  160 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~  160 (250)
                      +|++.+++..|..++.|...|++++++..|+..++..+|+|||..+.||||++++++|||+. +|.||++||+|+++.|+
T Consensus        81 pD~RvlV~~~rkiAe~Yy~vY~e~~pt~qlv~~~asvmQEyTqsgGvrPFGvslliaG~~~~-~p~LyQvdPSGsyf~wk  159 (233)
T KOG0181|consen   81 PDYRVLVHKSRKIAEQYYRVYGEPIPTTQLVQEVASVMQEYTQSGGVRPFGVSLLIAGWDEG-GPLLYQVDPSGSYFAWK  159 (233)
T ss_pred             CceeehhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhhcCCccccceEEEEeecCCC-ceeEEEECCccceeehh
Confidence            99999999999999999999999999999999999999999999999999999999999985 89999999999999999


Q ss_pred             EEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 025640          161 AAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH  240 (250)
Q Consensus       161 ~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~  240 (250)
                      ++|+|.+...++.+||++|+++|.+++++..|+..|++..+ ...+.++|||+++..++     |+++.+.||+++++.+
T Consensus       160 atA~Gkn~v~aktFlEkR~~edleldd~ihtailtlkE~fe-ge~~~~nieigv~~~~~-----F~~lt~~eI~d~l~~l  233 (233)
T KOG0181|consen  160 ATAMGKNYVNAKTFLEKRYNEDLELDDAIHTAILTLKESFE-GEMTAKNIEIGVCGENG-----FRRLTPAEIEDYLASL  233 (233)
T ss_pred             hhhhccCcchHHHHHHHHhccccccchHHHHHHHHHHHHhc-cccccCceEEEEecCCc-----eeecCHHHHHHHHhcC
Confidence            99999999999999999999999999999999999999997 56889999999998665     9999999999998753

>KOG0182 consensus 20S proteasome, regulatory subunit alpha type PSMA6/SCL1 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.6e-51  Score=325.82  Aligned_cols=236  Identities=35%  Similarity=0.615  Sum_probs=222.9

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcC-CccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGN-AGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMS   81 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~-g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~   81 (250)
                      .+||+++|+|||||||+|||||.||+++ |=|+||++++|++|+++.++.+.++...+ ....+|+|+.+|+|+.+|..+
T Consensus         7 agfDrhitIFspeGrLyQVEYafkAin~~gltsVavrgkDcavvvsqKkvpDKLld~~-tvt~~f~itk~ig~v~tG~~a   85 (246)
T KOG0182|consen    7 AGFDRHITIFSPEGRLYQVEYAFKAINQAGLTSVAVRGKDCAVVVTQKKVPDKLLDSS-TVTHLFRITKKIGCVITGMIA   85 (246)
T ss_pred             CCccceEEEECCCceEEeeehHHHHhhcCCCceEEEcCCceEEEEecccCcccccccc-cceeEEEeeccceEEEecCCc
Confidence            4899999999999999999999999999 55999999999999999999999998865 678999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceE
Q 025640           82 DANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKA  161 (250)
Q Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~  161 (250)
                      |++..+.++|.++.++++.||.+||++.||+.++++.|.|+|+..+||+||.+++.|+|++.||.+|.+||.|-+..+++
T Consensus        86 Dar~~v~rar~eAa~~~yk~Gyemp~DiL~k~~Ad~~QvytQ~a~mRplg~~~~~i~~D~E~gP~vYk~DpAGyy~g~kA  165 (246)
T KOG0182|consen   86 DARSQVQRARYEAAEFRYKYGYEMPCDILAKRMADKSQVYTQNAAMRPLGVAATLIGVDEERGPSVYKTDPAGYYYGFKA  165 (246)
T ss_pred             chHHHHHHHHHHHHhhhhhcCCCCCHHHHHHHHhhHHHHHhhhhhhcccceeEEEEEeccccCcceEeecCcccccccee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeCChHHHHHHHHhhCCCC--CCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          162 AAIGANNQAAQSILKQDYKDD--ISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       162 ~a~G~g~~~~~~~L~~~~~~~--~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      ++.|.....+.++||++|+++  .+.+|+++++..||..+.. -+.....+||++++++.   .+|+.|+.+||+..|..
T Consensus       166 taaG~Kq~e~tsfLEKk~Kk~~~~t~~e~ve~ai~al~~sl~-~Dfk~se~EVgvv~~~~---p~f~~Ls~~eie~hL~~  241 (246)
T KOG0182|consen  166 TAAGVKQQEATSFLEKKYKKDIDLTFEETVETAISALQSSLG-IDFKSSELEVGVVTVDN---PEFRILSAEEIEEHLQA  241 (246)
T ss_pred             eecccchhhHHHHHHHhhccCccchHHHHHHHHHHHHHHHHh-cccCCcceEEEEEEcCC---cceeeccHHHHHHHHHH
Confidence            999999999999999999977  7799999999999999987 34677899999999886   24999999999999988


Q ss_pred             hCCC
Q 025640          240 HGVT  243 (250)
Q Consensus       240 ~~~~  243 (250)
                      +.+.
T Consensus       242 IAEk  245 (246)
T KOG0182|consen  242 IAEK  245 (246)
T ss_pred             hhhc
Confidence            7653

>KOG0863 consensus 20S proteasome, regulatory subunit alpha type PSMA1/PRE5 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.1e-48  Score=314.56  Aligned_cols=232  Identities=35%  Similarity=0.558  Sum_probs=218.3

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      ++||...|+|||+|||+|||||++|++.|++.||++.++..||++-+|..+-+   +..++|||+|++|+++.++|+++|
T Consensus         4 nqyd~d~t~wsPqGrl~QvEya~EavkqGsatVGLks~thaVLvAl~r~~seL---ss~QkKi~~iD~h~g~siAGLt~D   80 (264)
T KOG0863|consen    4 NQYDNDVTTWSPQGRLHQVEYAMEAVKQGSATVGLKSRTHAVLVALKRAQSEL---SSHQKKIFKIDDHIGISIAGLTAD   80 (264)
T ss_pred             ccccCceeEECCcceehHHHHHHHHHhcccceEeecccceEEEeeeccchhHH---HHhhheeEecccccceEEeccCcc
Confidence            48999999999999999999999999999999999999999999999876655   347899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.|.+++|.++..+++.+++++++..|+..|++..|..||+.+.|||||.++++|+|+. ||+||.++|+|++.+++..
T Consensus        81 arvl~~Ylr~ec~~~~~~~~r~~pv~rl~~~l~~k~q~~Tq~ygrRpYGVGllv~gYDe~-G~hl~e~~Psg~v~e~~g~  159 (264)
T KOG0863|consen   81 ARVLSRYLRQECLNSRFIYGRPLPVLRLVEDLGDKAQENTQRYGRRPYGVGLLVAGYDES-GPHLYEFCPSGNVFECKGM  159 (264)
T ss_pred             hHHHHHHHHHHHhhhhhccCCcccHHHHHHHHHHHHhhhhhhhCCccccceEEEEeecCC-CceeEEEcCCccEEEEeee
Confidence            999999999999999999999999999999999999999999999999999999999984 9999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhCC--CCCCHHHHHHHHHHHHHHhhcC-CCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          163 AIGANNQAAQSILKQDYK--DDISREEAVQLALKVLSKTMDS-TSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~~--~~~s~~ea~~l~~~~l~~~~~~-~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      +||+.++.+.++||++..  ++++.||.+..++.||+.+... +..++.++.|+|+.+|.    +|..++.+++..++..
T Consensus       160 sIGsRSQsARTyLEr~~e~f~~~~~eELI~~gi~Alr~tlp~de~lt~~nvsI~Ivgkd~----pf~~~d~~~~~k~~~~  235 (264)
T KOG0863|consen  160 SIGSRSQSARTYLERNLEEFEDSSPEELIKHGIMALRETLPEDEDLTGENVSIAIVGKDE----PFTILDQKDVAKYVDL  235 (264)
T ss_pred             ecccchhhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcCcccccccceeEEEEEeCCC----ceEeecHHHHHHHHHH
Confidence            999999999999999875  7999999999999999999864 47899999999999997    6999999999987766


Q ss_pred             hCC
Q 025640          240 HGV  242 (250)
Q Consensus       240 ~~~  242 (250)
                      .++
T Consensus       236 ~~~  238 (264)
T KOG0863|consen  236 FKK  238 (264)
T ss_pred             hhc
Confidence            553

>TIGR03690 20S_bact_beta proteasome, beta subunit, bacterial type

Probab=100.00  E-value=9.2e-46  Score=310.01  Aligned_cols=209  Identities=20%  Similarity=0.292  Sum_probs=193.2

Q ss_pred             CCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Q 025640           30 NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQ  109 (250)
Q Consensus        30 ~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~  109 (250)
                      +|+|+|||+++||||||+|+|.++|.+..+++.+||++|+++++|+++|..+|++.+.+++|.++..|++.++.+++++.
T Consensus         1 ~G~T~igi~~kdgVvlaad~r~~~g~~~~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~~~~i~~~~   80 (219)
T TIGR03690         1 HGTTIVALTYPGGVLMAGDRRATQGNMIASRDVEKVYPTDEYSAVGIAGTAGLAIELVRLFQVELEHYEKIEGVPLTLDG   80 (219)
T ss_pred             CCcEEEEEEECCEEEEEECCccccCcEEEcCCcceEEEcCCcEEEEecccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH
Confidence            48999999999999999999999987777778999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhccccCCCcceeEEEEEEEEeCC-CCeEEEEECCCC-ceecceEEEEeCChHHHHHHHHhhCCCCCCHHH
Q 025640          110 LVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKN-YGFQLYMSDPSG-NYGGWKAAAIGANNQAAQSILKQDYKDDISREE  187 (250)
Q Consensus       110 la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~-~~~~Ly~vd~~G-~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~e  187 (250)
                      +++.|++++|.++ ...+|||++++||||||+. ++|+||.+||+| ++..++++|+|+|+.+++++||+.|+++||.+|
T Consensus        81 la~~ls~~~~~~~-~~~~rp~~v~~iiaG~D~~~~~~~Ly~~Dp~G~~~~~~~~~a~G~g~~~a~~~Le~~~~~~ms~ee  159 (219)
T TIGR03690        81 KANRLAAMVRGNL-PAAMQGLAVVPLLAGYDLDAGAGRIFSYDVTGGRYEERGYHAVGSGSVFAKGALKKLYSPDLDEDD  159 (219)
T ss_pred             HHHHHHHHHHhhh-hhccCCceEEEEEEEECCCCCCcEEEEEeCCCCeeecCCeEEEeccHHHHHHHHHhcCCCCcCHHH
Confidence            9999999998876 4458999999999999964 579999999999 577889999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCCCCCCCc-------EEEEEEEeCCCCceeEEECCHHHHHHHHHHhCCCC
Q 025640          188 AVQLALKVLSKTMDSTSLTSDK-------LELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQ  244 (250)
Q Consensus       188 a~~l~~~~l~~~~~~~~~~~~~-------iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~~~  244 (250)
                      |++++++||..+.+++..+++.       ++|++|++++     |+.++++||+.++.++.+.+
T Consensus       160 ai~l~~~al~~~~~~d~~s~~~~~~~~~~~ei~ii~~~g-----~~~l~~~ei~~~~~~~~~~~  218 (219)
T TIGR03690       160 ALRVAVEALYDAADDDSATGGPDLVRGIYPTVVVITADG-----ARRVPESELEELARAIVESR  218 (219)
T ss_pred             HHHHHHHHHHHHHhcccccCCcccccccccEEEEEccCc-----eEEcCHHHHHHHHHHHHhcc
Confidence            9999999999999998866664       3999998776     89999999999998877654

Members of this family are the beta subunit of the 20S proteasome as found in Actinobacteria such as Mycobacterium, Rhodococcus, and Streptomyces. In Streptomyces, maturation during proteasome assembly was shown to remove a 53-amino acid propeptide. Most of the length of the propeptide is not included in this model.

>PTZ00488 Proteasome subunit beta type-5; Provisional

Probab=100.00  E-value=2e-45  Score=312.17  Aligned_cols=209  Identities=18%  Similarity=0.236  Sum_probs=195.4

Q ss_pred             HhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCC
Q 025640           27 AIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMP  106 (250)
Q Consensus        27 a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~  106 (250)
                      .+.+|+|+|||+++||||||+|+|.+++.++..++.+||++|+++++++++|..+|++.+.+.+|.++..|++.++.+++
T Consensus        35 ~~~~G~T~IgIk~kdgVvlAaD~r~~~g~li~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~lr~~~~~y~~~~g~~is  114 (247)
T PTZ00488         35 EFAHGTTTLAFKYGGGIIIAVDSKATAGPYIASQSVKKVIEINPTLLGTMAGGAADCSFWERELAMQCRLYELRNGELIS  114 (247)
T ss_pred             ccCCCceEEEEEeCCEEEEEEecCcccCCEEEcCCcCceEEcCCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence            45789999999999999999999999888877778999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHH
Q 025640          107 VEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISRE  186 (250)
Q Consensus       107 ~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~  186 (250)
                      ++.+++.|++++|.++    ..|+.+++||||||+ .||+||++||+|++.+++++|+|.|+.+++++||+.|+++||.+
T Consensus       115 v~~la~~ls~~l~~~R----~~~~~v~~iiaG~D~-~gp~Ly~vDp~Gs~~~~~~~a~G~gs~~~~~~Le~~~k~dms~e  189 (247)
T PTZ00488        115 VAAASKILANIVWNYK----GMGLSMGTMICGWDK-KGPGLFYVDNDGTRLHGNMFSCGSGSTYAYGVLDAGFKWDLNDE  189 (247)
T ss_pred             HHHHHHHHHHHHHhcC----CCCeeEEEEEEEEeC-CCCEEEEEcCCcceeecCCEEEccCHHHHHHHHHhcCcCCCCHH
Confidence            9999999999998762    235556689999997 47999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhCCCCc
Q 025640          187 EAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQP  245 (250)
Q Consensus       187 ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~  245 (250)
                      ||++++++||+.+.+|+..++++++|++|+++|     ++.++++||+.++.++++.++
T Consensus       190 Eai~l~~kal~~~~~Rd~~sg~~~ei~iI~k~g-----~~~l~~~ei~~~l~~~~~~~~  243 (247)
T PTZ00488        190 EAQDLGRRAIYHATFRDAYSGGAINLYHMQKDG-----WKKISADDCFDLHQKYAAEKE  243 (247)
T ss_pred             HHHHHHHHHHHHHHHhccccCCCeEEEEEcCCc-----cEECCHHHHHHHHHHHhhhcc
Confidence            999999999999999999999999999999887     899999999999999886654

>TIGR03691 20S_bact_alpha proteasome, alpha subunit, bacterial type

Probab=100.00  E-value=2.2e-45  Score=308.48  Aligned_cols=207  Identities=22%  Similarity=0.277  Sum_probs=187.5

Q ss_pred             cchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHH
Q 025640           21 VEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYA  100 (250)
Q Consensus        21 veya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~  100 (250)
                      -|||++|+++|+|+|||+++||||||+|++.        ++.+||++|+||++|+++|+.+|++.+++.++.++..+++.
T Consensus        17 ~EYA~kav~~g~T~VGIk~kdgVVLaaek~~--------~~~~KI~~I~d~ig~~~sG~~~D~~~lv~~~r~~a~~~~~~   88 (228)
T TIGR03691        17 AELARKGIARGRSVVVLTYADGILFVAENPS--------RSLHKISELYDRIGFAAVGKYNEFENLRRAGIRYADMRGYS   88 (228)
T ss_pred             HHHHHHHHHcCCcEEEEEeCCeEEEEEecCC--------CCcCcEEEecCCEEEEEcCCHHHHHHHHHHHHHHHHHHhhh
Confidence            4999999999999999999999999999962        35789999999999999999999999999999999999999


Q ss_pred             hC-CCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeC-CCCeEEEEECCCCceecce-EEEEeCChHHHHHHHHh
Q 025640          101 YQ-EPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDK-NYGFQLYMSDPSGNYGGWK-AAAIGANNQAAQSILKQ  177 (250)
Q Consensus       101 ~~-~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~-~~~~~Ly~vd~~G~~~~~~-~~a~G~g~~~~~~~L~~  177 (250)
                      ++ .+++++.+++.+++.+..++ +++.|||+|++|++|||+ +.||+||.+||+|++.+++ ++|+|.+++.++++||+
T Consensus        89 ~~~~~~~v~~la~~~tq~~~~~~-~~~~RP~gvs~Li~G~d~~~~gp~Ly~vDpsG~~~~~~~~~aiG~gs~~a~~~Lek  167 (228)
T TIGR03691        89 YDRRDVTGRGLANAYAQTLGTIF-TEQQKPYEVEICVAEVGETPDQDQLYRITFDGSIVDERGFVVMGGTTEPIATALKE  167 (228)
T ss_pred             cCCCCccHHHHHHHHHhhccccc-ccccCcceEEEEEEEEcCCCCCCEEEEECCCCCceeccceEEECCChHHHHHHHHH
Confidence            98 68999999988887776666 567899999999999986 4589999999999999876 89999999999999999


Q ss_pred             hCCCCCCHHHHHHHHHHHHHHhh--cCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 025640          178 DYKDDISREEAVQLALKVLSKTM--DSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL  237 (250)
Q Consensus       178 ~~~~~~s~~ea~~l~~~~l~~~~--~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~  237 (250)
                      +|+++||++||++++++||+.+.  +++..++.++||++|++++. ...|++|+++||+.++
T Consensus       168 ~y~~~ms~eeai~la~~aL~~~~~~~r~~~~~~~iEv~ii~k~~~-~~~f~~l~~~ei~~~l  228 (228)
T TIGR03691       168 SYRDGLSLADALGLAVQALRAGGNGEKRELDAASLEVAVLDRSRP-RRAFRRITGEALERLL  228 (228)
T ss_pred             hcCCCCCHHHHHHHHHHHHHHHhccccccCCccceEEEEEeCCCC-ccceEECCHHHHHhhC
Confidence            99999999999999999999994  56679999999999997541 2359999999998764

Members of this family are the alpha subunit of the 20S proteasome as found in Actinobacteria such as Mycobacterium, Rhodococcus, and Streptomyces. In most Actinobacteria (an exception is Propionibacterium acnes), the proteasome is accompanied by a system of tagging proteins for degradation with Pup.

>cd03758 proteasome_beta_type_2 proteasome beta type-2 subunit

Probab=100.00  E-value=1.8e-45  Score=302.68  Aligned_cols=186  Identities=24%  Similarity=0.263  Sum_probs=178.4

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.+++.+..+++.+|||+|+++++|+++|..+|++.+.+.++.++..|++.++++++++.++
T Consensus         2 ~t~igi~~~dgVvlaad~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~i~~~~la   81 (193)
T cd03758           2 ETLIGIKGKDFVILAADTSAARSILVLKDDEDKIYKLSDHKLMACSGEAGDRLQFAEYIQKNIQLYKMRNGYELSPKAAA   81 (193)
T ss_pred             ceEEEEEeCCEEEEEEcCccccCcEEEecCcccEEEeCCCeEEEEccchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            68999999999999999999998877777899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.+|.+++. + |||++++||+|||++.+|+||++||+|++.+++++|+|+|+.+++++||+.|+++||.+||+++
T Consensus        82 ~~l~~~~~~~~~~-~-rP~~~~~li~G~d~~~~p~Ly~~d~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~ms~eeai~l  159 (193)
T cd03758          82 NFTRRELAESLRS-R-TPYQVNLLLAGYDKVEGPSLYYIDYLGTLVKVPYAAHGYGAYFCLSILDRYYKPDMTVEEALEL  159 (193)
T ss_pred             HHHHHHHHHHhhc-C-CCeEEEEEEEEEcCCCCcEEEEECCCcceEECCeeEEeecHHHHHHHHHhccCCCCCHHHHHHH
Confidence            9999999887654 3 8999999999999766899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      +.+||+.+.+|++.++++++|++|+++|
T Consensus       160 ~~~a~~~~~~rd~~~~~~i~i~ii~~~g  187 (193)
T cd03758         160 MKKCIKELKKRFIINLPNFTVKVVDKDG  187 (193)
T ss_pred             HHHHHHHHHHhccccCCceEEEEEcCCC
Confidence            9999999999999999999999999887

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis.Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03759 proteasome_beta_type_3 proteasome beta type-3 subunit

Probab=100.00  E-value=2.9e-45  Score=301.99  Aligned_cols=187  Identities=16%  Similarity=0.194  Sum_probs=177.7

Q ss_pred             cCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHH
Q 025640           29 GNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVE  108 (250)
Q Consensus        29 ~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~  108 (250)
                      .+|+|+|||+++||||||+|++.++++++.+++.+|||+|++|++|+++|..+|++.+.+.+|.++..|++.++.+++++
T Consensus         1 ~~G~t~igik~~dgVvlaad~~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~   80 (195)
T cd03759           1 YNGGAVVAMAGKDCVAIASDLRLGVQQQTVSTDFQKVFRIGDRLYIGLAGLATDVQTLAQKLRFRVNLYRLREEREIKPK   80 (195)
T ss_pred             CCCceEEEEEcCCEEEEEEccccccCCEeEecCCCeEEEeCCCEEEEccchHHHHHHHHHHHHHHHHHHHHHhCCCCCHH
Confidence            37999999999999999999999999988777789999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce-EEEEeCChHHHHHHHHhhCCCCCCHHH
Q 025640          109 QLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK-AAAIGANNQAAQSILKQDYKDDISREE  187 (250)
Q Consensus       109 ~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~-~~a~G~g~~~~~~~L~~~~~~~~s~~e  187 (250)
                      .+++.|++.++.  +  +.+||+|++||||||++++|+||++||+|++..++ ++|+|.|+++++++||+.|+++||.+|
T Consensus        81 ~la~~l~~~ly~--~--r~~P~~v~~ii~G~D~~~~p~Ly~~D~~G~~~~~~~~~a~G~g~~~~~~~Le~~~~~~~s~~e  156 (195)
T cd03759          81 TFSSLISSLLYE--K--RFGPYFVEPVVAGLDPDGKPFICTMDLIGCPSIPSDFVVSGTASEQLYGMCESLWRPDMEPDE  156 (195)
T ss_pred             HHHHHHHHHHHH--h--cCCCceEEEEEEEEcCCCCEEEEEEcCCCcccccCCEEEEcccHHHHHHHHHhccCCCCCHHH
Confidence            999999998854  3  25899999999999977789999999999998877 999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          188 AVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       188 a~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      |++++++||+.+.+|++.++++++|++|+++|
T Consensus       157 a~~l~~~~l~~~~~rd~~~~~~~~i~ii~~~g  188 (195)
T cd03759         157 LFETISQALLSAVDRDALSGWGAVVYIITKDK  188 (195)
T ss_pred             HHHHHHHHHHHHHhhCcccCCceEEEEEcCCc
Confidence            99999999999999999999999999999887

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03760 proteasome_beta_type_4 proteasome beta type-4 subunit

Probab=100.00  E-value=6.6e-45  Score=300.40  Aligned_cols=188  Identities=18%  Similarity=0.181  Sum_probs=177.7

Q ss_pred             CCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHH-HHHHHhCCCCCHH
Q 025640           30 NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQ-RYTYAYQEPMPVE  108 (250)
Q Consensus        30 ~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~-~~~~~~~~~~~~~  108 (250)
                      .|+|+|||+++||||||+|+|.+++.+..+++.+|||+|+++++|+++|..+|++.+.+++|.++. .+++.++.+++++
T Consensus         1 ~G~T~igi~~kdgVvlaad~r~~~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~   80 (197)
T cd03760           1 TGTSVIAIKYKDGVIIAADTLGSYGSLARFKNVERIFKVGDNTLLGASGDYADFQYLKRLLDQLVIDDECLDDGHSLSPK   80 (197)
T ss_pred             CCceEEEEEeCCcEEEEEcCcccccceeecCCCCcEEEecCcEEEEeCcchHHHHHHHHHHHHHHHHHHHHhCCCCCCHH
Confidence            489999999999999999999997777777788999999999999999999999999999999986 5667899999999


Q ss_pred             HHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCC--CCCHH
Q 025640          109 QLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD--DISRE  186 (250)
Q Consensus       109 ~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~--~~s~~  186 (250)
                      .++++|++.+  |++++++|||+|++||||||++++|+||++||+|++.+++++|+|+|+.+++++||+.|++  +||++
T Consensus        81 ~la~~i~~~~--y~~~~~~rP~~v~~iiaG~D~~~gp~Ly~~D~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~~ms~e  158 (197)
T cd03760          81 EIHSYLTRVL--YNRRSKMNPLWNTLVVGGVDNEGEPFLGYVDLLGTAYEDPHVATGFGAYLALPLLREAWEKKPDLTEE  158 (197)
T ss_pred             HHHHHHHHHH--HHHhhcCCCceEEEEEEEEcCCCCEEEEEEcCCccEEECCEeEEccHHHHHHHHHHhhcCCCCCCCHH
Confidence            9999999985  5777789999999999999976689999999999999999999999999999999999999  99999


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          187 EAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       187 ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      ||++++.+||+.+.+|+..++++++|++|+++|
T Consensus       159 ea~~l~~~~l~~~~~rd~~~~~~~~i~ii~~~g  191 (197)
T cd03760         159 EARALIEECMKVLYYRDARSINKYQIAVVTKEG  191 (197)
T ss_pred             HHHHHHHHHHHHHHHhccccCCceEEEEECCCC
Confidence            999999999999999999999999999999987

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis.Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03761 proteasome_beta_type_5 proteasome beta type-5 subunit

Probab=100.00  E-value=1.6e-44  Score=295.97  Aligned_cols=183  Identities=20%  Similarity=0.291  Sum_probs=176.5

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.+++.++.+++.+|||+|++|++|+++|..+|++.+.+.+|.++..|++.++.+++++.++
T Consensus         1 tT~igi~~kdgVvla~d~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i~~~~la   80 (188)
T cd03761           1 TTTLAFIFQGGVIVAVDSRATAGSYIASQTVKKVIEINPYLLGTMAGGAADCQYWERVLGRECRLYELRNKERISVAAAS   80 (188)
T ss_pred             CcEEEEEECCEEEEEEcCCccCCcEEEcCCcceEEEccCcEEEEeCccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            58999999999999999999998888777889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++++|.+++    .||++++||||||+ .||+||++||+|++.+++++|+|.|+.+++++||+.|+++||.+||+++
T Consensus        81 ~~ls~~l~~~~~----~~~~v~~li~G~D~-~g~~L~~~dp~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~s~eea~~l  155 (188)
T cd03761          81 KLLSNMLYQYKG----MGLSMGTMICGWDK-TGPGLYYVDSDGTRLKGDLFSVGSGSTYAYGVLDSGYRYDLSVEEAYDL  155 (188)
T ss_pred             HHHHHHHHhcCC----CCeEEEEEEEEEeC-CCCEEEEEcCCceEEEcCeEEEcccHHHHHHHHHhcCCCCCCHHHHHHH
Confidence            999999998864    58999999999997 5899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      +.+||+.+.+|+..++++++|++|+++|
T Consensus       156 ~~~~l~~~~~rd~~sg~~~~v~ii~~~g  183 (188)
T cd03761         156 ARRAIYHATHRDAYSGGNVNLYHVREDG  183 (188)
T ss_pred             HHHHHHHHHHhcccCCCCeEEEEEcCCc
Confidence            9999999999999999999999999887

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>TIGR03634 arc_protsome_B proteasome endopeptidase complex, archaeal, beta subunit

Probab=100.00  E-value=4.9e-44  Score=292.42  Aligned_cols=184  Identities=28%  Similarity=0.472  Sum_probs=177.3

Q ss_pred             CccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 025640           31 AGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQL  110 (250)
Q Consensus        31 g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l  110 (250)
                      |+|+|||+++||||||+|+|.+++.++.+++.+|||+|+++++|+++|..+|++.+.++++.++..|+..++.+++++.+
T Consensus         1 G~t~igi~~~dgVvla~d~~~~~~~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~   80 (185)
T TIGR03634         1 GTTTVGIKCKDGVVLAADKRASMGNFVASKNAKKVFQIDDYIAMTIAGSVGDAQSLVRILKAEAKLYELRRGRPMSVKAL   80 (185)
T ss_pred             CCcEEEEEeCCEEEEEEcCcccCCCEEecCCcccEEEcCCCEEEEcCchHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH
Confidence            78999999999999999999998888877789999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHH
Q 025640          111 VQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQ  190 (250)
Q Consensus       111 a~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~  190 (250)
                      ++.|++.+|.+    ++|||+|++||||||++ ||+||.+||+|++.+++++++|.++.+++++||+.|+++||++||++
T Consensus        81 a~~l~~~~~~~----~~rP~~v~~ivaG~d~~-g~~Ly~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~s~~ea~~  155 (185)
T TIGR03634        81 ATLLSNILNSN----RFFPFIVQLLVGGVDEE-GPHLYSLDPAGGIIEDDYTATGSGSPVAYGVLEDEYREDMSVEEAKK  155 (185)
T ss_pred             HHHHHHHHHhc----CCCCeEEEEEEEEEeCC-CCEEEEECCCCCeEECCEEEEcCcHHHHHHHHHhcCCCCCCHHHHHH
Confidence            99999999876    57999999999999975 89999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          191 LALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       191 l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      ++.+||+.+.+|++.++++++|++|+++|
T Consensus       156 l~~~~l~~~~~r~~~~~~~~~v~ii~~~g  184 (185)
T TIGR03634       156 LAVRAIKSAIERDVASGNGIDVAVITKDG  184 (185)
T ss_pred             HHHHHHHHHHHhcccCCCCEEEEEEcCCC
Confidence            99999999999999999999999999876

This protein family describes the archaeal proteasome beta subunit, homologous to both the alpha subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated.

>cd03757 proteasome_beta_type_1 proteasome beta type-1 subunit

Probab=100.00  E-value=4.7e-44  Score=298.33  Aligned_cols=188  Identities=23%  Similarity=0.324  Sum_probs=178.9

Q ss_pred             hcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCH
Q 025640           28 IGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPV  107 (250)
Q Consensus        28 ~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~  107 (250)
                      +++|+|+|||+++||||||+|++.++++++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++.++++
T Consensus         5 ~~~G~Tvigik~~dgVvlaaD~r~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~i~~   84 (212)
T cd03757           5 TDNGGTVLAIAGNDFAVIAGDTRLSEGYSILSRDSPKIFKLTDKCVLGSSGFQADILALTKRLKARIKMYKYSHNKEMST   84 (212)
T ss_pred             cCCCccEEEEEcCCEEEEEECCccccCCEeEeCCCCeEEEcCCCEEEEccchHHHHHHHHHHHHHHHHHHhHHhCCCCCH
Confidence            57899999999999999999999999998877788999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCC-------
Q 025640          108 EQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK-------  180 (250)
Q Consensus       108 ~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~-------  180 (250)
                      +.+++.+++.++..    +.+||++++||||||++++|+||.+||.|++.+++++|+|+|+.+++++||+.|+       
T Consensus        85 ~~la~~ls~~ly~~----R~~P~~~~~iiaG~D~~~~p~Ly~~D~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~~~~~~  160 (212)
T cd03757          85 EAIAQLLSTILYSR----RFFPYYVFNILAGIDEEGKGVVYSYDPVGSYERETYSAGGSASSLIQPLLDNQVGRKNQNNV  160 (212)
T ss_pred             HHHHHHHHHHHHhh----cCCCeEEEEEEEEEcCCCCEEEEEEcCccCeeecCEEEEeecHHHHHHHHHHHHHhhccCcC
Confidence            99999999998643    2479999999999997668999999999999999999999999999999999975       


Q ss_pred             --CCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          181 --DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       181 --~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                        ++||++||++++.+||+.+.+|++.++++++|++|+++|
T Consensus       161 ~~~~ms~eea~~l~~~~l~~~~~rd~~sg~~i~i~iit~~g  201 (212)
T cd03757         161 ERTPLSLEEAVSLVKDAFTSAAERDIYTGDSLEIVIITKDG  201 (212)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHhCcccCCCEEEEEEcCCC
Confidence              899999999999999999999999999999999999987

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03764 proteasome_beta_archeal Archeal proteasome, beta subunit

Probab=100.00  E-value=2e-43  Score=289.51  Aligned_cols=187  Identities=28%  Similarity=0.476  Sum_probs=178.9

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|.++.+++.+||++|+++++++++|..+|++.+.+.++.++..|++.++++++++.++
T Consensus         1 tt~iai~~~dgvvia~d~r~~~g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~   80 (188)
T cd03764           1 TTTVGIVCKDGVVLAADKRASMGNFIASKNVKKIFQIDDKIAMTIAGSVGDAQSLVRILKAEARLYELRRGRPMSIKALA   80 (188)
T ss_pred             CcEEEEEeCCEEEEEEccccccCCEEecCCcccEEEccCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            58999999999999999999998888778899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.+|.+    ++|||+|++||||||+ ++|+||.+||+|++.+++++|+|+|+++++++|++.|+++|+++||+++
T Consensus        81 ~~i~~~~~~~----~~~P~~~~~lvaG~d~-~~~~ly~~D~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~~~~ea~~l  155 (188)
T cd03764          81 TLLSNILNSS----KYFPYIVQLLIGGVDE-EGPHLYSLDPLGSIIEDKYTATGSGSPYAYGVLEDEYKEDMTVEEAKKL  155 (188)
T ss_pred             HHHHHHHHhc----CCCCcEEEEEEEEEeC-CCCEEEEECCCCCEEEcCEEEEcCcHHHHHHHHHhcCCCCCCHHHHHHH
Confidence            9999999876    4799999999999998 5899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEEC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVC  228 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~  228 (250)
                      +++||+.+.+|++.++++++|++|+++|     ++.+
T Consensus       156 ~~~~l~~~~~rd~~~~~~i~i~iv~~~g-----~~~~  187 (188)
T cd03764         156 AIRAIKSAIERDSASGDGIDVVVITKDG-----YKEL  187 (188)
T ss_pred             HHHHHHHHHhhcCCCCCcEEEEEECCCC-----eEeC
Confidence            9999999999999999999999999887     6655

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme for non-lysosomal protein degradation in both the cytosol and the nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are both members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03765 proteasome_beta_bacterial Bacterial proteasome, beta subunit

Probab=100.00  E-value=1.8e-43  Score=297.33  Aligned_cols=199  Identities=19%  Similarity=0.180  Sum_probs=178.7

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEec----CceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCC-CCC
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKID----DHVACAVAGIMSDANILINTARVQAQRYTYAYQE-PMP  106 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~----~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~-~~~  106 (250)
                      +-+|||+++||||||+|+|+++++...+ +.+||++|+    +|++|+.||..+|++.+.+.+|.++..|++.++. +++
T Consensus         1 ~~~vGIk~kdGVVLaadkr~~~~l~~~~-~~~KI~~I~~~~d~~I~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~~~~   79 (236)
T cd03765           1 TYCLGIKLDAGLVFASDSRTNAGVDNIS-TYRKMFVFSVPGERVIVLLTAGNLATTQAVISLLQRDLEDPEETNLLNAPT   79 (236)
T ss_pred             CeEEEEEeCCeEEEEEccCccCCCcccc-ccceEEEecCCCCCEEEEEcCCcHHHHHHHHHHHHHHHHhhHHhhCCCCCC
Confidence            3589999999999999999999987766 689999998    8999999999999999999999999999999999 899


Q ss_pred             HHHHHHHHHHHHhh-ccccCC-----CcceeEEEEEEEEeCCCCeEEEEECCCCceecc----eEEEEeCChHHHHHHHH
Q 025640          107 VEQLVQSLCDTKQG-YTQFGG-----LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW----KAAAIGANNQAAQSILK  176 (250)
Q Consensus       107 ~~~la~~l~~~~~~-~~~~~~-----~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~----~~~a~G~g~~~~~~~L~  176 (250)
                      ++.+|+.+++.++. +++..+     .|||+|++||||||++.||+||++||+|++.++    +++|+|. +.+++++||
T Consensus        80 v~~la~~i~~~l~~~~~q~~~~~~~~~rp~gvslIigG~D~~~Gp~LY~idpsG~~~e~~a~~~~~AiG~-~~~a~~~Le  158 (236)
T cd03765          80 MFDAARYVGETLREVQEQDREALKKAGIDFSASFILGGQIKGEEPRLFLIYPQGNFIEATPDTPFLQIGE-TKYGKPILD  158 (236)
T ss_pred             HHHHHHHHHHHHHHHHhhcccccccCCcceEEEEEEEeEECCCCCEEEEECCCCCEEeecCCCceeeeCC-chhhHHHHH
Confidence            99999999998544 445443     489999999999997678999999999999998    5689996 689999999


Q ss_pred             hhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHH
Q 025640          177 QDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEA  232 (250)
Q Consensus       177 ~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~e  232 (250)
                      ++|+++||++||++++++||..+.+|+..++++|+|++|+++|-.....++++.++
T Consensus       159 k~yk~~ms~eeai~la~~al~~a~~rd~~sg~~iev~vI~k~G~~~~~~~~~~~~~  214 (236)
T cd03765         159 RVITPDTSLEDAAKCALVSMDSTMRSNLSVGPPLDLLVYERDSLQVGHYRRIEEDD  214 (236)
T ss_pred             HhcCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCEEEEEEECCCeeeeeeEEecCCC
Confidence            99999999999999999999999999999999999999999985443445665554

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03762 proteasome_beta_type_6 proteasome beta type-6 subunit

Probab=100.00  E-value=9e-43  Score=285.68  Aligned_cols=183  Identities=19%  Similarity=0.270  Sum_probs=175.7

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|.+..+++.+||++|+++++|+++|..+|++.+.+.++.++..|+..++.+++++.++
T Consensus         1 ~t~igi~~~dgVvla~D~r~~~g~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~a   80 (188)
T cd03762           1 TTIIAVEYDGGVVLGADSRTSTGSYVANRVTDKLTQLHDRIYCCRSGSAADTQAIADYVRYYLDMHSIELGEPPLVKTAA   80 (188)
T ss_pred             CeEEEEEECCeEEEEEcccccCCceEEcCCcccEEEccCCEEEEecccHHHHHHHHHHHHHHHHHhHHhhCCCCCHHHHH
Confidence            58999999999999999999998887777899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.+|.++     |||++++||||||++.||+||.+||.|++.+++++++|+++.+++++||+.|+++||++||+++
T Consensus        81 ~~l~~~~~~~~-----~~~~~~~ii~G~d~~~gp~ly~~d~~G~~~~~~~~~~G~g~~~~~~~Le~~~~~~~s~~ea~~l  155 (188)
T cd03762          81 SLFKNLCYNYK-----EMLSAGIIVAGWDEQNGGQVYSIPLGGMLIRQPFAIGGSGSTYIYGYVDANYKPGMTLEECIKF  155 (188)
T ss_pred             HHHHHHHHhcc-----ccceeeEEEEEEcCCCCcEEEEECCCCCEEecCEEEEcccHHHHHHHHHhcCCCCCCHHHHHHH
Confidence            99999998763     7899999999999756899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      +++||+.+.+|++.++++++|++|+++|
T Consensus       156 ~~~al~~~~~rd~~~~~~~~i~~i~~~g  183 (188)
T cd03762         156 VKNALSLAMSRDGSSGGVIRLVIITKDG  183 (188)
T ss_pred             HHHHHHHHHHhccccCCCEEEEEECCCC
Confidence            9999999999999999999999999887

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd03763 proteasome_beta_type_7 proteasome beta type-7 subunit

Probab=100.00  E-value=8.7e-43  Score=285.97  Aligned_cols=182  Identities=22%  Similarity=0.306  Sum_probs=174.6

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|.+..+++.+|||+|+++++|+++|..+|++.+.+.++.++..|++.++++++++.++
T Consensus         1 tt~igi~~~dgvvlaad~r~~~g~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (189)
T cd03763           1 TTIVGVVFKDGVVLGADTRATEGPIVADKNCEKIHYIAPNIYCCGAGTAADTEAVTNMISSNLELHRLNTGRKPRVVTAL   80 (189)
T ss_pred             CeEEEEEECCeEEEEEcCCcccCceEEcCCccceEEecCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            58999999999999999999999888777889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.|++.+|.+.     .||+|++||||||+. ||+||.+||.|++.+++++|+|.++.+++++|++.|+++||++||+++
T Consensus        81 ~~l~~~l~~~~-----~p~~v~~ivaG~d~~-g~~ly~~d~~G~~~~~~~~a~G~~~~~~~~~L~~~~~~~ls~~ea~~l  154 (189)
T cd03763          81 TMLKQHLFRYQ-----GHIGAALVLGGVDYT-GPHLYSIYPHGSTDKLPFVTMGSGSLAAMSVLEDRYKPDMTEEEAKKL  154 (189)
T ss_pred             HHHHHHHHHcC-----CccceeEEEEeEcCC-CCEEEEECCCCCEEecCEEEEcCCHHHHHHHHHhhcCCCCCHHHHHHH
Confidence            99999998763     399999999999974 799999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      +++||+.+.+|++.++++++|++|+++|
T Consensus       155 ~~~~l~~~~~rd~~~~~~~~v~ii~~~g  182 (189)
T cd03763         155 VCEAIEAGIFNDLGSGSNVDLCVITKDG  182 (189)
T ss_pred             HHHHHHHHHHhcCcCCCceEEEEEcCCc
Confidence            9999999999999999999999999987

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>cd01912 proteasome_beta proteasome beta subunit

Probab=100.00  E-value=3.2e-42  Score=282.55  Aligned_cols=184  Identities=27%  Similarity=0.387  Sum_probs=177.5

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|++.++++....++.+|||+|+++++++++|+.+|++.+.++++.++..|++.++++++++.++
T Consensus         1 tt~i~i~~~dgVvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~   80 (189)
T cd01912           1 TTIVGIKGKDGVVLAADTRASAGSLVASRNFDKIFKISDNILLGTAGSAADTQALTRLLKRNLRLYELRNGRELSVKAAA   80 (189)
T ss_pred             CcEEEEEeCCEEEEEEcCCcccCcEEEcCCcCcEEEccCCEEEEccccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            58999999999999999999999988667899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.++.+++    |||++++||||||++++|+||.+||.|++.+++++++|.++++++++|++.|+++||++||+++
T Consensus        81 ~~l~~~~~~~~~----~P~~~~~iv~G~d~~~~~~l~~id~~G~~~~~~~~a~G~~~~~~~~~Le~~~~~~~s~~ea~~~  156 (189)
T cd01912          81 NLLSNILYSYRG----FPYYVSLIVGGVDKGGGPFLYYVDPLGSLIEAPFVATGSGSKYAYGILDRGYKPDMTLEEAVEL  156 (189)
T ss_pred             HHHHHHHHhcCC----CCeEEEEEEEEEcCCCCeEEEEECCCCCeEecCEEEEcccHHHHHHHHHhccCCCCCHHHHHHH
Confidence            999999988765    8999999999999866899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      +++||+.+.++++.++++++|++|+++|
T Consensus       157 ~~~~l~~~~~~d~~~~~~~~v~vi~~~g  184 (189)
T cd01912         157 VKKAIDSAIERDLSSGGGVDVAVITKDG  184 (189)
T ss_pred             HHHHHHHHHHhcCccCCcEEEEEECCCC
Confidence            9999999999999999999999999887

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.

>PF00227 Proteasome: Proteasome subunit; InterPro: IPR001353 ATP-dependent protease complexes are present in all three kingdoms of life, where they rid the cell of misfolded or damaged proteins and control the level of certain regulatory proteins

Probab=100.00  E-value=1.2e-42  Score=285.03  Aligned_cols=188  Identities=40%  Similarity=0.656  Sum_probs=179.8

Q ss_pred             hcCCccEEEEEeCCEEEEEEEcccCCCcccccCC-cCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCC
Q 025640           28 IGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS-TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMP  106 (250)
Q Consensus        28 ~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~-~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~  106 (250)
                      +++|+|+|||+++||||||+|++.++|....+.+ .+|||+|+++++++++|..+|++.+.++++.++..+++.++.+++
T Consensus         1 v~~G~t~vgi~~~dgvvla~d~~~~~g~~~~~~~~~~ki~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~   80 (190)
T PF00227_consen    1 VNNGTTVVGIKGKDGVVLAADKRISYGSKLRSPNTVDKIFKINDNIIIGFSGLTADFQYLIRRLREEAQEYRFSYGRPIS   80 (190)
T ss_dssp             HHTSBEEEEEEESSEEEEEEEEEEEETTEEEESSTSSSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTC
T ss_pred             CCCCeEEEEEEECCEEEEEEccccccccccccccccceeeeccCcceeeccccccchHHHHhhhcccchhhhhccCcccc
Confidence            4789999999999999999999999887775444 699999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecc-eEEEEeCChHHHHHHHHhhCCCCCCH
Q 025640          107 VEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW-KAAAIGANNQAAQSILKQDYKDDISR  185 (250)
Q Consensus       107 ~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~-~~~a~G~g~~~~~~~L~~~~~~~~s~  185 (250)
                      ++.+++.++..++.++++.+.||+++++|++|||++++|+||.+||+|++.++ +++++|+|+++++++|++.|+++|++
T Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~p~~~~~li~G~d~~~~~~l~~vd~~G~~~~~~~~~aiG~g~~~~~~~l~~~~~~~~~~  160 (190)
T PF00227_consen   81 PEYLAKAIASLIQNYTYRSGRRPYGVSLLIAGYDEDGGPQLYSVDPSGSYIECKRFAAIGSGSQFAQPILEKLYKPDLSL  160 (190)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTSTTSEEEEEEEEETTTEEEEEEEETTSEEEEBSSEEEESTTHHHHHHHHHHHHTTTSSH
T ss_pred             chhhhhhhHHHHhhhcccccccCccccceeeeeccccccceeeeccccccccccccccchhcchhhhHHHHhhccCCCCH
Confidence            99999999999999999999999999999999998777999999999999999 69999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          186 EEAVQLALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       186 ~ea~~l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      +||++++++||+.+.+++..++++++|++|
T Consensus       161 ~ea~~~~~~~l~~~~~~d~~~~~~~~v~vi  190 (190)
T PF00227_consen  161 EEAIELALKALKEAIDRDILSGDNIEVAVI  190 (190)
T ss_dssp             HHHHHHHHHHHHHHHHHBTTSTSEEEEEEE
T ss_pred             HHHHHHHHHHHHHHHhhCCccCCeEEEEEC
Confidence            999999999999999999999999999986

They include the proteasome in Eukaryotes, Archaea, and Actinomycetales and the HslVU (ClpQY, clpXP) complex in other eubacteria. Genes homologous to eubacterial HslV (ClpQ) and HslU (ClpY, clpX) have also been demonstrated in to be present in the genome of trypanosomatid protozoa []. The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). The prokaryotic ATP-dependent proteasome is coded for by the heat-shock locus VU (HslVU). It consists of HslV, the protease (MEROPS peptidase subfamily T1B), and HslU, IPR004491 from INTERPRO, the ATPase and chaperone belonging to the AAA/Clp/Hsp100 family. The crystal structure of Thermotoga maritima HslV has been determined to 2.1-A resolution. The structure of the dodecameric enzyme is well conserved compared to those from Escherichia coli and Haemophilus influenzae [, ]. This entry contains threonine peptidases and non-peptidase homologs belong to MEROPS peptidase family T1 (proteasome family, clan PB(T)). The family consists of the protease components of the archaeal and bacterial proteasomes and the alpha and beta subunits of the eukaryotic proteasome. ; GO: 0004298 threonine-type endopeptidase activity, 0051603 proteolysis involved in cellular protein catabolic process, 0005839 proteasome core complex; PDB: 3KRD_1 3H6F_M 2FHH_F 3HF9_F 2FHG_D 3HFA_B 3H6I_K 3MI0_A 3MFE_1 3MKA_F ....

>cd01906 proteasome_protease_HslV proteasome_protease_HslV

Probab=100.00  E-value=2.5e-41  Score=275.33  Aligned_cols=182  Identities=47%  Similarity=0.727  Sum_probs=175.2

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|++.++++....++.+|||+|+++++|+++|..+|++.+.+.+++++..|++.++.+++++.++
T Consensus         1 tt~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~   80 (182)
T cd01906           1 TTIVGIKGKDGVVLAADKRVTSGLLVASSTVEKIFKIDDHIGCAFAGLAADAQTLVERLRKEAQLYRLRYGEPIPVEALA   80 (182)
T ss_pred             CcEEEEEeCCEEEEEEecccCCcCeecCCCcceEEEECCCEEEEEeeCHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            58999999999999999999999888667899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.+|.+++.  .||+++++||||||++.+|+||.+||.|++.+++++|+|.++.+++++|++.|+++||.+||+++
T Consensus        81 ~~l~~~~~~~~~~--~~p~~~~~lv~G~d~~~~~~Ly~id~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  158 (182)
T cd01906          81 KLLANLLYEYTQS--LRPLGVSLLVAGVDEEGGPQLYSVDPSGSYIEYKATAIGSGSQYALGILEKLYKPDMTLEEAIEL  158 (182)
T ss_pred             HHHHHHHHHhCCC--ccChheEEEEEEEeCCCCcEEEEECCCCCEeeccEEEECCCcHHHHHHHHHHccCCCCHHHHHHH
Confidence            9999999999876  89999999999999866899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      +++||+.+.+++..++.+++|++|
T Consensus       159 ~~~~l~~~~~~~~~~~~~~~i~ii  182 (182)
T cd01906         159 ALKALKSALERDLYSGGNIEVAVI  182 (182)
T ss_pred             HHHHHHHHHcccCCCCCCEEEEEC
Confidence            999999999999999999999875

This group contains the eukaryotic proteosome alpha and beta subunits and the prokaryotic protease hslV subunit. Proteasomes are large multimeric self-compartmentalizing proteases, involved in the clearance of misfolded proteins, the breakdown of regulatory proteins, and the processing of proteins such as the preparation of peptides for immune presentation. Two main proteasomal types are distinguished by their different tertiary structures: the eukaryotic/archeal 20S proteasome and the prokaryotic proteasome-like heat shock protein encoded by heat shock locus V, hslV. The proteasome core particle is a highly conserved cylindrical structure made up of non-identical subunits that have their active sites on the inner walls of a large central cavity. The proteasome subunits of bacteria, archaea, and eukaryotes all share a conserved Ntn (N terminal nucleophile) hydrolase fold and a catalytic mechanism involving an N-terminal nucleo

>KOG0177 consensus 20S proteasome, regulatory subunit beta type PSMB2/PRE1 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=6.4e-39  Score=251.24  Aligned_cols=186  Identities=21%  Similarity=0.223  Sum_probs=180.2

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      .+++||++.|+|++|+|+...++++..+.+.+|++.|+++++|+++|..+|+.++.++++++++.|++.+|.+++|+..|
T Consensus         2 e~llGIkg~dfvilAsDt~~~~si~~~k~~~dK~~~ls~~~lm~~~Ge~GDt~qF~eyi~~Ni~LYkirnGyeLSp~~aa   81 (200)
T KOG0177|consen    2 ETLLGIKGPDFVILASDTSAARSILVLKDDHDKIHRLSDHILMATVGEAGDTVQFTEYIQKNIQLYKIRNGYELSPSAAA   81 (200)
T ss_pred             ceEEEeecCCEEEEeecchhhcceEEecccccceEEeccceeeeeecCCCceehHHHHHHhhhhHHhhhcCCcCCHHHHH
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +++...+..+.+  ..+||.|++|+||+|++.||.||++|..|+..+.++++.|.++.++.++|++.|+|+||.+||+++
T Consensus        82 hFtR~~La~~LR--sr~~yqV~~LvaGYd~~~gp~L~~iDyla~~~~vpy~~hGy~~~f~~sIlDr~Y~pdmt~eea~~l  159 (200)
T KOG0177|consen   82 HFTRRELAESLR--SRTPYQVNILVAGYDPEEGPELYYIDYLATLVSVPYAAHGYGSYFCLSILDRYYKPDMTIEEALDL  159 (200)
T ss_pred             HHHHHHHHHHHh--cCCCceEEEEEeccCCCCCCceeeehhhhhcccCCcccccchhhhhHHHHHhhhCCCCCHHHHHHH
Confidence            999988887776  368999999999999998999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      ..+|+.++.+|...+-.++.|.+|+|+|
T Consensus       160 mkKCv~El~kRlvin~~~f~v~IVdkdG  187 (200)
T KOG0177|consen  160 MKKCVLELKKRLVINLPGFIVKIVDKDG  187 (200)
T ss_pred             HHHHHHHHHHhcccCCCCcEEEEEcCCC
Confidence            9999999999999999999999999998

>KOG0179 consensus 20S proteasome, regulatory subunit beta type PSMB1/PRE7 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.5e-37  Score=245.71  Aligned_cols=190  Identities=22%  Similarity=0.316  Sum_probs=180.9

Q ss_pred             HHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCC
Q 025640           26 EAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPM  105 (250)
Q Consensus        26 ~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~  105 (250)
                      .-..||+|+|||.+.|++|+|+|+|.++++.+.+++..|||+++|+++++.+|+++|+..|...++..+..|+..++..|
T Consensus        24 PY~~NGGT~vaIaG~dFavvA~DTR~s~gy~I~sR~~~Ki~~l~D~~vl~~sGF~aD~l~L~k~i~~r~~~Y~~~h~k~m  103 (235)
T KOG0179|consen   24 PYEDNGGTTVAIAGEDFAVVAGDTRMSSGYNINSRDQSKIFKLGDNIVLGSSGFYADTLALVKVIKSRIKQYEHDHNKKM  103 (235)
T ss_pred             ccccCCceEEEEcCCceEEEecccccccceeeeccccchheeccCceEEecccchhhHHHHHHHHHHHHHHHhhcccccc
Confidence            44589999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCC-----
Q 025640          106 PVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK-----  180 (250)
Q Consensus       106 ~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~-----  180 (250)
                      +...+|++|+..++..    +++||.+..||+|+|+++++.+|+.||.|++.+..+.|-|+++.+++++|+....     
T Consensus       104 s~~s~A~lls~~LY~k----RFFPYYv~~ilaGiDeeGKG~VySyDPvGsyer~~~~AgGsa~~mI~PfLDnQi~~kn~~  179 (235)
T KOG0179|consen  104 SIHSAAQLLSTILYSK----RFFPYYVFNILAGIDEEGKGAVYSYDPVGSYERVTCRAGGSAASMIQPFLDNQIGHKNQN  179 (235)
T ss_pred             cHHHHHHHHHHHHhhc----ccccceeeeeeecccccCceeEEeecCCcceeeeeeecCCcchhhhhhhhhhhccCcCcc
Confidence            9999999999999743    5899999999999999989999999999999999999999999999999997542     


Q ss_pred             ------CCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          181 ------DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       181 ------~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                            ..+|+|+|+.|+.++|..+.+|++.+++.++|+|++++|
T Consensus       180 ~e~~~~~~Ls~e~ai~lv~d~F~SAaERdI~tGD~l~i~I~tk~g  224 (235)
T KOG0179|consen  180 LENAERTPLSLERAIRLVKDAFTSAAERDIYTGDKLEICIITKDG  224 (235)
T ss_pred             cccCcccccCHHHHHHHHHHHhhhhhhcccccCCcEEEEEEecCC
Confidence                  468999999999999999999999999999999999997

>KOG0174 consensus 20S proteasome, regulatory subunit beta type PSMB6/PSMB9/PRE3 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=6.6e-38  Score=246.22  Aligned_cols=207  Identities=17%  Similarity=0.293  Sum_probs=189.7

Q ss_pred             HhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCC
Q 025640           27 AIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMP  106 (250)
Q Consensus        27 a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~  106 (250)
                      .++.|+|++|+.+++||||++|+|++.|.++.++-.+|+.+|.|+|+||.||.++|+|.+.+.++.++..|...++.+++
T Consensus        15 evstGTTImAv~y~gGVvlGaDSRTs~GayvanRvtDKlT~itD~i~cCRSGSAADtQaiaD~~~Y~L~~~~~q~~~~p~   94 (224)
T KOG0174|consen   15 EVSTGTTIMAVEYDGGVVLGADSRTSTGAYVANRVTDKLTPITDNIYCCRSGSAADTQAIADIVRYHLELYTIQENKPPL   94 (224)
T ss_pred             ccccCceEEEEEEcCcEEEeccCCccchHHHHhhhcccceeccccEEEecCCchhhHHHHHHHHHHHHHHhhhhcCCCch
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHH
Q 025640          107 VEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISRE  186 (250)
Q Consensus       107 ~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~  186 (250)
                      +...|....++.++|+.     -+.+.+||||||+..|.++|.+---|+..+.++..-|+|+.|++++++..|+|+|++|
T Consensus        95 v~~aA~l~r~~~Y~~re-----~L~AgliVAGwD~~~gGqVY~iplGG~l~rq~~aIgGSGStfIYGf~D~~~r~nMt~E  169 (224)
T KOG0174|consen   95 VHTAASLFREICYNYRE-----MLSAGLIVAGWDEKEGGQVYSIPLGGSLTRQPFAIGGSGSTFIYGFCDANWRPNMTLE  169 (224)
T ss_pred             HHHHHHHHHHHHHhCHH-----hhhcceEEeecccccCceEEEeecCceEeecceeeccCCceeeeeeehhhcCCCCCHH
Confidence            99999999999888753     3889999999999889999999444555577777778999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhC
Q 025640          187 EAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHG  241 (250)
Q Consensus       187 ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~  241 (250)
                      |++.+..+++..++.||-.+|+.|.+.+|+++|   +..+.+.++++..+.....
T Consensus       170 E~~~fvk~Av~lAi~rDGsSGGviR~~~I~~~G---ver~~~~~d~~~~~~v~t~  221 (224)
T KOG0174|consen  170 ECVRFVKNAVSLAIERDGSSGGVIRLVIINKAG---VERRFFPGDKLGQFAVETP  221 (224)
T ss_pred             HHHHHHHHHHHHHHhccCCCCCEEEEEEEccCC---ceEEEecCCccccccccCC
Confidence            999999999999999999999999999999998   5678888888876655443

>KOG0175 consensus 20S proteasome, regulatory subunit beta type PSMB5/PSMB8/PRE2 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.1e-34  Score=237.11  Aligned_cols=211  Identities=19%  Similarity=0.276  Sum_probs=198.4

Q ss_pred             hcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCH
Q 025640           28 IGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPV  107 (250)
Q Consensus        28 ~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~  107 (250)
                      ..+|+|.+|++++.|||+|+|+|.+.|.++.+...+||.+|+++++-.++|-++|++..-+.+..+|..|++.+++.|++
T Consensus        68 ~~hGTTTLAF~f~~GvivAvDSRAs~G~YIasqtv~KVIeIn~ylLGTmAGgAADCqfWer~L~kecRL~eLRnkeriSV  147 (285)
T KOG0175|consen   68 FAHGTTTLAFKFKGGVIVAVDSRASAGSYIASQTVKKVIEINPYLLGTMAGGAADCQFWERVLAKECRLHELRNKERISV  147 (285)
T ss_pred             ecCCceEEEEEecCcEEEEEeccccccceeechhhceeeeechhhhhcccCcchhhHHHHHHHHHHHHHHHHhcCcceeh
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHH
Q 025640          108 EQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREE  187 (250)
Q Consensus       108 ~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~e  187 (250)
                      ...++.|+++++.|+   ++. +.+..+|+|||+ .||.||+||..|+-...+-+++|+|+.+++++|++.|+++|+.+|
T Consensus       148 saASKllsN~~y~Yk---GmG-LsmGtMi~G~Dk-~GP~lyYVDseG~Rl~G~~FSVGSGs~yAYGVLDsgYr~dls~eE  222 (285)
T KOG0175|consen  148 SAASKLLSNMVYQYK---GMG-LSMGTMIAGWDK-KGPGLYYVDSEGTRLSGDLFSVGSGSTYAYGVLDSGYRYDLSDEE  222 (285)
T ss_pred             HHHHHHHHHHHhhcc---Ccc-hhheeeEeeccC-CCCceEEEcCCCCEecCceEeecCCCceeEEeeccCCCCCCCHHH
Confidence            999999999998875   332 788899999998 499999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhCCCCcccc
Q 025640          188 AVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQPAAE  248 (250)
Q Consensus       188 a~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~  248 (250)
                      |.+|++.++..+..||.++|+.+.++.|..+|     |.+++..++..+..++.+..+.|.
T Consensus       223 A~~L~rrAI~hAThRDaySGG~vnlyHv~edG-----W~~v~~~Dv~~L~~~~~e~~~~~~  278 (285)
T KOG0175|consen  223 AYDLARRAIYHATHRDAYSGGVVNLYHVKEDG-----WVKVSNTDVSELHYHYYEVAPPEA  278 (285)
T ss_pred             HHHHHHHHHHHHHhcccccCceEEEEEECCcc-----ceecCCccHHHHHHHHHHhcCccc
Confidence            99999999999999999999999999999998     999999999999777766655543

>KOG0185 consensus 20S proteasome, regulatory subunit beta type PSMB4/PRE4 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=7.9e-35  Score=235.10  Aligned_cols=226  Identities=18%  Similarity=0.202  Sum_probs=198.2

Q ss_pred             ccccCCCCccc------ccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            9 TTIFSPEGRLY------QVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         9 ~~~f~p~G~l~------qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      +++|.|.|.+.      .+..-+...-.|+++||++++||||||+|+..++|.+...++.+|+++|+|++++|++|..+|
T Consensus        13 ~~~f~~~~~~m~~a~~~~~qrt~~p~vTGTSVla~ky~~GVviaaD~lgSYGslaR~~nVeRi~kVgdntllG~sGdisD   92 (256)
T KOG0185|consen   13 PGTFYPSGSLMENAGDYPIQRTLNPIVTGTSVLALKYKDGVVIAADTLGSYGSLARYKNVERIFKVGDNTLLGASGDISD   92 (256)
T ss_pred             CCcCcCccchhhhccCCCcccccCceeccceEEEEEecCceEEEecccccchhhhhhcCceeeEEecCceEEecCccHHH
Confidence            56777776542      222223345679999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH-HHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceE
Q 025640           83 ANILINTARVQAQRYT-YAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKA  161 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~-~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~  161 (250)
                      +|.|.+.+.....+.+ +.-+..+.|+.++.+|.+.++.  +++.+.|+..+++|||+++++.|+|-.+|-.|...+.+.
T Consensus        93 ~Q~i~r~L~~l~iedn~~~Dg~~l~Pk~ih~yltrvlY~--rRsKmnPlwntlvVgGv~~~g~~~lg~V~~~G~~Y~~~~  170 (256)
T KOG0185|consen   93 FQYIQRVLEQLVIEDNRLDDGQSLGPKAIHSYLTRVLYA--RRSKMNPLWNTLVVGGVDNTGEPFLGYVDLLGVAYESPV  170 (256)
T ss_pred             HHHHHHHHHHHHhcccccccccccChHHHHHHHHHHHHH--hhhccCchhhheeEeeecCCCCeeEEEEeeccccccCch
Confidence            9999999977766643 4556899999999999999974  567899999999999999988899999999999999999


Q ss_pred             EEEeCChHHHHHHHHhhCC---CCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 025640          162 AAIGANNQAAQSILKQDYK---DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLV  238 (250)
Q Consensus       162 ~a~G~g~~~~~~~L~~~~~---~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~  238 (250)
                      +|+|.|+..+.++|++.|.   ++++.+||.+++.+||+.+..||+.+.++++|++|+.+|     +..-.+..|..-|+
T Consensus       171 vATGfg~hLa~P~lR~~~~~k~~~~s~eeA~~li~~cMrVL~YRD~ra~n~fqva~v~~eG-----v~i~~p~qv~~~W~  245 (256)
T KOG0185|consen  171 VATGFGAHLALPLLRDEWEKKGEDLSREEAEALIEKCMRVLYYRDARASNEFQVATVDEEG-----VTISKPYQVKTNWD  245 (256)
T ss_pred             hhhhhHHHhhhHHHHHhhhccchhhHHHHHHHHHHHHHHHHhccccccccceEEEEEcccc-----eEecCceeeeecch
Confidence            9999999999999999997   789999999999999999999999999999999999987     67777777766555


Q ss_pred             HhC
Q 025640          239 KHG  241 (250)
Q Consensus       239 ~~~  241 (250)
                      -.+
T Consensus       246 fa~  248 (256)
T KOG0185|consen  246 FAE  248 (256)
T ss_pred             hhh
Confidence            443

>KOG0173 consensus 20S proteasome, regulatory subunit beta type PSMB7/PSMB10/PUP1 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.8e-34  Score=234.16  Aligned_cols=190  Identities=22%  Similarity=0.338  Sum_probs=175.7

Q ss_pred             HHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCC
Q 025640           24 AMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQE  103 (250)
Q Consensus        24 a~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~  103 (250)
                      +.++.+.|+|++|+.++||||+++|+|.+.|..+.+++..||+.|.++|+||.+|-++|..++...+..+++.+.++.++
T Consensus        30 ~p~~tkTGTtIvgv~~k~gvIlgADtRaT~G~IvaDKnC~KIH~ia~~IyccGAGtAADte~vt~m~ss~l~Lh~l~t~R  109 (271)
T KOG0173|consen   30 APKATKTGTTIVGVIFKDGVILGADTRATEGPIVADKNCEKIHFIAPNIYCCGAGTAADTEMVTRMISSNLELHRLNTGR  109 (271)
T ss_pred             CCcccccCcEEEEEEeCCeEEEeecccccCCCeeecchhHHHhhcccceEEccCCchhhHHHHHHHHHHHHHHHHhccCC
Confidence            34567889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCC
Q 025640          104 PMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDI  183 (250)
Q Consensus       104 ~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~  183 (250)
                      .+.+-...++|.+.+..|-   +  -.++.+|++|+|.. ||+||.+.|.|+...-+|.++|+|+..+.++||.+|+|+|
T Consensus       110 ~~rVv~A~~mlkQ~LFrYq---G--~IgA~LiiGGvD~T-GpHLy~i~phGStd~~Pf~alGSGslaAmsvlEsr~k~dl  183 (271)
T KOG0173|consen  110 KPRVVTALRMLKQHLFRYQ---G--HIGAALILGGVDPT-GPHLYSIHPHGSTDKLPFTALGSGSLAAMSVLESRWKPDL  183 (271)
T ss_pred             CCceeeHHHHHHHHHHHhc---C--cccceeEEccccCC-CCceEEEcCCCCcCccceeeeccchHHHHHHHHHhcCccc
Confidence            9887777777777665542   3  38999999999995 9999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          184 SREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       184 s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      ++|||++|+.+|+..-+..|..+|+++++|+|++.+
T Consensus       184 t~eea~~Lv~eAi~AGi~nDLgSGsnvdlcVI~~~~  219 (271)
T KOG0173|consen  184 TKEEAIKLVCEAIAAGIFNDLGSGSNVDLCVITKKG  219 (271)
T ss_pred             CHHHHHHHHHHHHHhhhccccCCCCceeEEEEeCCC
Confidence            999999999999999999899999999999999554

>PRK05456 ATP-dependent protease subunit HslV; Provisional

Probab=100.00  E-value=5.6e-32  Score=217.24  Aligned_cols=167  Identities=19%  Similarity=0.188  Sum_probs=145.9

Q ss_pred             CccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEe-cCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Q 025640           31 AGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKI-DDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQ  109 (250)
Q Consensus        31 g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~  109 (250)
                      |+|+|||+++||||||+|+|++.|.++.+++.+||++| +++++|+++|..+|++.|.+.++.++..|+.  +.   ++.
T Consensus         1 gtTivgi~~~dgVvlaaD~r~s~g~~v~~~~~~KI~~i~~d~i~~~~aG~~aD~q~l~~~l~~~~~~y~~--~~---~~~   75 (172)
T PRK05456          1 GTTILAVRRNGKVAIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEEHQG--NL---LRA   75 (172)
T ss_pred             CcEEEEEEECCEEEEEECCceEeCcEEEcCCCceEEEeCCCCEEEEEeccHHHHHHHHHHHHHHHHHccC--cc---HHH
Confidence            68999999999999999999999999999999999999 9999999999999999999999999998872  22   355


Q ss_pred             HHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecc--eEEEEeCChHHHHHHHHhhCC-CCCCHH
Q 025640          110 LVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW--KAAAIGANNQAAQSILKQDYK-DDISRE  186 (250)
Q Consensus       110 la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~--~~~a~G~g~~~~~~~L~~~~~-~~~s~~  186 (250)
                      .++....+..    ....+|+.+++|++  |.   |+||.+||.|++.+.  +++++|+|+.++.++||+.|+ ++|   
T Consensus        76 ~a~l~~~l~~----~~~~~~l~~~~lv~--d~---~~ly~id~~G~~~~~~~~~~a~GSGs~~a~g~ld~~y~~~~m---  143 (172)
T PRK05456         76 AVELAKDWRT----DRYLRRLEAMLIVA--DK---EHSLIISGNGDVIEPEDGIIAIGSGGNYALAAARALLENTDL---  143 (172)
T ss_pred             HHHHHHHHHh----ccCCCccEEEEEEE--cC---CcEEEECCCCcEeccCCCeEEEecCHHHHHHHHHHhhhcCCC---
Confidence            5544433211    11246888999995  32   689999999999766  899999999999999999999 999   


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCcEEEEE
Q 025640          187 EAVQLALKVLSKTMDSTSLTSDKLELAE  214 (250)
Q Consensus       187 ea~~l~~~~l~~~~~~~~~~~~~iei~i  214 (250)
                      ||++++++|++.+.+||..++++|+|-.
T Consensus       144 eA~~la~kai~~A~~Rd~~sg~~i~v~~  171 (172)
T PRK05456        144 SAEEIAEKALKIAADICIYTNHNITIEE  171 (172)
T ss_pred             CHHHHHHHHHHHHHHhCeeCCCcEEEEE
Confidence            9999999999999999999999998865

>KOG0180 consensus 20S proteasome, regulatory subunit beta type PSMB3/PUP3 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=4.5e-32  Score=209.60  Aligned_cols=188  Identities=15%  Similarity=0.195  Sum_probs=179.5

Q ss_pred             hcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCH
Q 025640           28 IGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPV  107 (250)
Q Consensus        28 ~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~  107 (250)
                      ..||+++||+.++++|.||+|.|....+...+++++|||+++|++++|.+|++.|++.+.+.++.....|++..+++|.|
T Consensus         5 synGg~vvAM~gk~cvaIa~D~RlG~q~~tistdf~ki~~igdr~y~GL~glatDvqtl~~~~~fr~nLy~lre~R~i~P   84 (204)
T KOG0180|consen    5 SYNGGSVVAMAGKNCVAIASDLRLGVQSQTISTDFQKIFKIGDRLYLGLTGLATDVQTLLERLRFRKNLYELREEREIKP   84 (204)
T ss_pred             eecCceEEEEeCCceEEEEeccccceeeeeeeccchhheecCCeeEEeccccchhHHHHHHHHHHHHhHHHhhhhcccCc
Confidence            36899999999999999999999988777778899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCcee-cceEEEEeCChHHHHHHHHhhCCCCCCHH
Q 025640          108 EQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYG-GWKAAAIGANNQAAQSILKQDYKDDISRE  186 (250)
Q Consensus       108 ~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~-~~~~~a~G~g~~~~~~~L~~~~~~~~s~~  186 (250)
                      +.++..+|..+++.    +..||.+.-+|||+|++..|++...|..|... ..+|++.|.+++.+++..|..|+|+|..|
T Consensus        85 ~~~s~mvS~~lYek----RfgpYf~~PvVAGl~~~~kPfIc~mD~IGc~~~~~DFVvsGTa~e~L~GmCE~ly~pnmepd  160 (204)
T KOG0180|consen   85 ETFSSMVSSLLYEK----RFGPYFTEPVVAGLDDDNKPFICGMDLIGCIDAPKDFVVSGTASEQLYGMCEALYEPNMEPD  160 (204)
T ss_pred             HHHHHHHHHHHHHh----hcCCcccceeEeccCCCCCeeEeecccccCcCccCCeEEecchHHHHHHHHHHhcCCCCCHH
Confidence            99999999999876    47899999999999998899999999999987 56899999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          187 EAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       187 ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      +..+.+.++|-.+.+||+.+|+...+.+|+++.
T Consensus       161 ~LFetisQa~Lna~DRDalSGwGa~vyiI~kdk  193 (204)
T KOG0180|consen  161 ELFETISQALLNAVDRDALSGWGAVVYIITKDK  193 (204)
T ss_pred             HHHHHHHHHHHhHhhhhhhccCCeEEEEEccch
Confidence            999999999999999999999999999999986

>cd01913 protease_HslV Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome

Probab=100.00  E-value=2.6e-31  Score=211.96  Aligned_cols=165  Identities=18%  Similarity=0.173  Sum_probs=143.1

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecC-ceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDD-HVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQL  110 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~-~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l  110 (250)
                      +|+|||+++||||||+|+|.+.|.++.+++.+||++|++ +++||++|..+|++.|.++++.+++.|+...++     .+
T Consensus         1 tTivgi~~~dgVvlaaD~r~t~G~~v~~~~~~Ki~~i~d~~i~~~~aG~~aD~~~l~~~~~~~~~~y~~~~~~-----~a   75 (171)
T cd01913           1 TTILAVRKNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVIAGFAGSTADAFTLFERFEAKLEQYPGNLLR-----AA   75 (171)
T ss_pred             CeEEEEEECCEEEEEECCceEeccEEEcCCcceEEEeCCCCEEEEecccHHHHHHHHHHHHHHHHHhhchHHH-----HH
Confidence            589999999999999999999999999999999999999 999999999999999999999999999877663     34


Q ss_pred             HHHHHHHHhhccccCCCccee-EEEEEEEEeCCCCeEEEEECCCCceecc--eEEEEeCChHHHHHHHHhhCCCC-CCHH
Q 025640          111 VQSLCDTKQGYTQFGGLRPFG-VSFLFAGWDKNYGFQLYMSDPSGNYGGW--KAAAIGANNQAAQSILKQDYKDD-ISRE  186 (250)
Q Consensus       111 a~~l~~~~~~~~~~~~~rP~~-~~~iv~G~d~~~~~~Ly~vd~~G~~~~~--~~~a~G~g~~~~~~~L~~~~~~~-~s~~  186 (250)
                      ++.+..++ .+    ..+|+. +.+++++|+     +||.+||.|++.+.  ++.++|+|+.+++++||..|+++ |+  
T Consensus        76 a~l~~~l~-~~----~~~~~l~a~~iv~~~~-----~ly~id~~G~~ie~~~~~~a~GSGS~ya~g~ld~~yk~~~ms--  143 (171)
T cd01913          76 VELAKDWR-TD----RYLRRLEAMLIVADKE-----HTLLISGNGDVIEPDDGIAAIGSGGNYALAAARALLDHTDLS--  143 (171)
T ss_pred             HHHHHHHH-hc----cCcCceEEEEEEeCCC-----cEEEECCCCCEeccCCCeEEEeCCHHHHHHHHHHhhccCCCC--
Confidence            44433332 11    234554 777776554     79999999999998  49999999999999999999995 99  


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCcEEEEE
Q 025640          187 EAVQLALKVLSKTMDSTSLTSDKLELAE  214 (250)
Q Consensus       187 ea~~l~~~~l~~~~~~~~~~~~~iei~i  214 (250)
                       +.+++.++++.+.+||..++++|++-.
T Consensus       144 -~~~la~~Av~~A~~rd~~tg~~i~~~~  170 (171)
T cd01913         144 -AEEIARKALKIAADICIYTNHNITVEE  170 (171)
T ss_pred             -HHHHHHHHHHHHHhhCcccCCCEEEEe
Confidence             669999999999999999999998764

HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the interior walls of the cavity. HslV shares significant sequence and structural similarity with the proteasomal beta-subunit and both are members of the Ntn-family of hydrolases. HslV has a nucleophilic threonine residue at its N-terminus that is exposed after processing of the propeptide and is directly involved in active site catalysis.

>TIGR03692 ATP_dep_HslV ATP-dependent protease HslVU, peptidase subunit

Probab=99.97  E-value=8.3e-31  Score=209.07  Aligned_cols=166  Identities=19%  Similarity=0.206  Sum_probs=142.1

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEe-cCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKI-DDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQL  110 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l  110 (250)
                      +|+|||+++||||||+|+|.+.|.++.+++.+||++| +++++||++|..+|++.|.++++.+++.|+...     .+.+
T Consensus         1 tTivgi~~~dgVvlaaD~r~s~g~~v~~~~~~Ki~~i~~d~i~~~~aG~~aD~q~l~~~~~~~~~~y~~~~-----~~~~   75 (171)
T TIGR03692         1 TTILAVRRNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEEYQGNL-----TRAA   75 (171)
T ss_pred             CeEEEEEECCEEEEEECCceEeceEEEcCCCCeEEEeCCCCEEEEecchHHHHHHHHHHHHHHHHHccCch-----HHHH
Confidence            5899999999999999999999999999999999999 599999999999999999999999999887632     3555


Q ss_pred             HHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecc--eEEEEeCChHHHHHHHHhhC-CCCCCHHH
Q 025640          111 VQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW--KAAAIGANNQAAQSILKQDY-KDDISREE  187 (250)
Q Consensus       111 a~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~--~~~a~G~g~~~~~~~L~~~~-~~~~s~~e  187 (250)
                      ++.+...    ..+...+.+.+.+|++||+     +||.+||.|++.+.  ++.++|+|+.+++++||..| +++|+   
T Consensus        76 a~l~~~~----~~~~~~~~l~a~~iv~~~~-----~ly~i~~~G~~ie~~~~~~a~GSGS~~a~g~ld~~y~~~~~s---  143 (171)
T TIGR03692        76 VELAKDW----RTDRYLRRLEAMLIVADKE-----TSLLISGTGDVIEPEDGIAAIGSGGNYALAAARALLRNTDLS---  143 (171)
T ss_pred             HHHHHHH----hhcccccccEEEEEEEcCC-----CEEEEcCCCcEeccCCCeEEEeCCHHHHHHHHHHhhhcCCCC---
Confidence            5555542    1111223344777776553     79999999999996  69999999999999999999 57788   


Q ss_pred             HHHHHHHHHHHhhcCCCCCCCcEEEEE
Q 025640          188 AVQLALKVLSKTMDSTSLTSDKLELAE  214 (250)
Q Consensus       188 a~~l~~~~l~~~~~~~~~~~~~iei~i  214 (250)
                      |++++.++++.+++||..++++|+|-.
T Consensus       144 a~~la~~Av~~A~~rd~~sg~~i~v~~  170 (171)
T TIGR03692       144 AEEIAREALKIAADICIYTNHNITIEE  170 (171)
T ss_pred             HHHHHHHHHHHHHhhCccCCCCEEEEe
Confidence            999999999999999999999999864

The ATP-dependent protease HslVU, a complex of hexameric HslU active as a protein-unfolding ATPase and dodecameric HslV, the catalytic threonine protease.

>cd01901 Ntn_hydrolase The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid

Probab=99.97  E-value=3.5e-29  Score=198.53  Aligned_cols=162  Identities=40%  Similarity=0.558  Sum_probs=155.6

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||++++|+|||+|++.+.+.........|+++++++++++++|..+|++.+.+++++++..|++.++.++++..++
T Consensus         1 ~t~i~i~~~~gvila~d~~~~~~~~~~~~~~~ki~~~~~~~~~~~sG~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (164)
T cd01901           1 STSVAIKGKGGVVLAADKRLSSGLPVAGSPVIKIGKNEDGIAWGLAGLAADAQTLVRRLREALQLYRLRYGEPISVVALA   80 (164)
T ss_pred             CcEEEEEeCCEEEEEEecccCccCeecCCCcceEEEecCCeEEEEecChHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            58999999999999999999999988666889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecc-eEEEEeCChHHHHHHHHhhCCCCCCHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW-KAAAIGANNQAAQSILKQDYKDDISREEAVQ  190 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~-~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~  190 (250)
                      +.+++.++.+++   .||+++++||+|+|+ ++|+||.+||.|++.+. .++++|.++.++.++|++.|+++|+.+|+++
T Consensus        81 ~~~~~~~~~~~~---~~p~~~~~iiag~~~-~~~~l~~id~~g~~~~~~~~~~~G~~~~~~~~~l~~~~~~~~~~~~~~~  156 (164)
T cd01901          81 KELAKLLQVYTQ---GRPFGVNLIVAGVDE-GGGNLYYIDPSGPVIENPGAVATGSRSQRAKSLLEKLYKPDMTLEEAVE  156 (164)
T ss_pred             HHHHHHHHHhcC---CCCcceEEEEEEEcC-CCCEEEEECCCcCEeecCcEEEECCCCHHHHHHHHHHhcCCCCHHHHHH
Confidence            999999998877   799999999999998 68999999999999999 9999999999999999999999999999999


Q ss_pred             HHHHHHH
Q 025640          191 LALKVLS  197 (250)
Q Consensus       191 l~~~~l~  197 (250)
                      ++.+||.
T Consensus       157 ~~~~~l~  163 (164)
T cd01901         157 LALKALK  163 (164)
T ss_pred             HHHHHHh
Confidence            9999986

N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either t

>COG3484 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]

Probab=99.69  E-value=3.8e-16  Score=124.54  Aligned_cols=187  Identities=19%  Similarity=0.184  Sum_probs=147.9

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEec----CceEEEEeCchHHHHHHHHHHHHHHHHHHH-HhCCCCC
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKID----DHVACAVAGIMSDANILINTARVQAQRYTY-AYQEPMP  106 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~----~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~-~~~~~~~  106 (250)
                      +-|||++...|.|+++|+|++.|....+ .++|+|.-.    .-++++.+|+.+-.|.+++.+.+..+...- .--...+
T Consensus         2 TYCv~l~l~~GlVf~sDsRTNAGvD~is-tfkKl~~~~~pGdRvlvl~taGNLA~tQaV~~ll~e~~~~d~~~~L~n~~s   80 (255)
T COG3484           2 TYCVGLILDFGLVFGSDSRTNAGVDYIS-TFKKLFVFELPGDRVLVLCTAGNLAITQAVLHLLDERIQRDDGDSLLNIPS   80 (255)
T ss_pred             ceEEEEEeccceEEecccccccCchHHH-HHHHHhhccCCCceEEEEEecCccHHHHHHHHHHHHHhhccchhhhhcchh
Confidence            5699999999999999999999987655 567777652    356788999999999999998776652111 1112234


Q ss_pred             HHHHHHHHHHHHhhccccC------CCcceeEEEEEEEEeCCCCeEEEEECCCCceec----ceEEEEeCChHHHHHHHH
Q 025640          107 VEQLVQSLCDTKQGYTQFG------GLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGG----WKAAAIGANNQAAQSILK  176 (250)
Q Consensus       107 ~~~la~~l~~~~~~~~~~~------~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~----~~~~a~G~g~~~~~~~L~  176 (250)
                      +-..+..+....++-.-+.      ..--|.|++|++|.-..+.|.||.+.|.|++.+    .+|..+|... +.+++|+
T Consensus        81 m~eattlvgetvrEv~~rds~~leka~~dfn~sfllGGQI~G~pp~Ly~IYpqGNFIqaT~etpf~QiGEtK-YGKPild  159 (255)
T COG3484          81 MYEATTLVGETVREVQARDSPALEKAGIDFNCSFLLGGQIKGEPPRLYLIYPQGNFIQATPETPFLQIGETK-YGKPILD  159 (255)
T ss_pred             HHHHHHHHHHHHHHHHhccCchhhccCcceeEEEEEcceecCCCceeEEEccCCCeeecCCCCceeEccccc-cCchhhh
Confidence            4455555554443221111      123489999999998866789999999999984    5899999877 7999999


Q ss_pred             hhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCC
Q 025640          177 QDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPS  220 (250)
Q Consensus       177 ~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~  220 (250)
                      +.+.-+++++|+.++++-+|....+.+..+|-++++-++++|..
T Consensus       160 R~i~~~~pLeea~kcaLvS~DSTlkSNiSVGlPldLl~~e~ds~  203 (255)
T COG3484         160 RTITYDTPLEEAAKCALVSFDSTLKSNISVGLPLDLLVYEADSF  203 (255)
T ss_pred             hhhhccCCHHHHhhheEEecchhhhccccccCCceeEEEeccce
Confidence            99999999999999999999999999999999999999999874

>COG5405 HslV ATP-dependent protease HslVU (ClpYQ), peptidase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.59  E-value=1.7e-14  Score=111.23  Aligned_cols=170  Identities=20%  Similarity=0.240  Sum_probs=139.9

Q ss_pred             CCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecC-ceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHH
Q 025640           30 NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDD-HVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVE  108 (250)
Q Consensus        30 ~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~-~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~  108 (250)
                      .++|+++++.++-++||.|.+.+-|..+.+.+..|+.+|.+ +++.|++|..+|+..|.+.+...++.|+         .
T Consensus         3 h~TTiv~vr~~gkv~iagDGQVtlG~tvmK~narKvRkl~~gkvlaGFAGstADaftLfe~fe~kle~~~---------g   73 (178)
T COG5405           3 HMTTIVAVRKNGKVVIAGDGQVTLGNTVMKGNARKVRRLYNGKVLAGFAGSTADAFTLFERFEAKLEQYQ---------G   73 (178)
T ss_pred             eeEEEEEEeeCCeEEEecCceEeecceeeeccHHHHHHHcCCcEEEEecccchhHHHHHHHHHHHHHHcc---------C
Confidence            57899999999999999999999999999888888888765 8999999999999999999998888764         1


Q ss_pred             HHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecc--eEEEEeCChHHHHHHHHhhCC-CCCCH
Q 025640          109 QLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW--KAAAIGANNQAAQSILKQDYK-DDISR  185 (250)
Q Consensus       109 ~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~--~~~a~G~g~~~~~~~L~~~~~-~~~s~  185 (250)
                      .|.+..-++.+.|+....+|.+.+-++|+  |+   -.+|-+...|-..+.  +.++||+|..++.+..+..+. +++| 
T Consensus        74 ~L~raavelaKdwr~Dk~lr~LEAmllVa--d~---~~il~isG~gdV~epe~~~~aIGSGgnyAl~AarAl~~~~~ls-  147 (178)
T COG5405          74 DLFRAAVELAKDWRTDKYLRKLEAMLLVA--DK---THILIITGNGDVIEPEDDIIAIGSGGNYALSAARALMENTELS-  147 (178)
T ss_pred             cHHHHHHHHHHhhhhhhHHHHHhhheeEe--CC---CcEEEEecCcceecCCCCeEEEcCCchHHHHHHHHHHhccCCC-
Confidence            24444445555555555567788888887  33   347888888988743  599999999999999988876 4777 


Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCcEEEEEEE
Q 025640          186 EEAVQLALKVLSKTMDSTSLTSDKLELAEVF  216 (250)
Q Consensus       186 ~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~  216 (250)
                        |.+++.++|..+.+-+.+++++|.|-.+.
T Consensus       148 --A~eIa~~sl~iA~eiciyTN~ni~ve~l~  176 (178)
T COG5405         148 --AREIAEKSLKIAGDICIYTNHNIVVEELR  176 (178)
T ss_pred             --HHHHHHHHHhhhheEEEecCCcEEEEEee
Confidence              77899999999998888999998887764

>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3

Probab=99.56  E-value=9.5e-16  Score=80.10  Aligned_cols=23  Identities=70%  Similarity=1.174  Sum_probs=22.3

Q ss_pred             CCCCccccCCCCcccccchHHHH
Q 025640            5 YDSRTTIFSPEGRLYQVEYAMEA   27 (250)
Q Consensus         5 yd~~~~~f~p~G~l~qveya~~a   27 (250)
                      ||+++|+|||||||+|||||.||
T Consensus         1 YD~~~t~FSp~Grl~QVEYA~~A   23 (23)
T PF10584_consen    1 YDRSITTFSPDGRLFQVEYAMKA   23 (23)
T ss_dssp             TSSSTTSBBTTSSBHHHHHHHHH
T ss_pred             CCCCceeECCCCeEEeeEeeecC
Confidence            89999999999999999999987

4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....

>PF09894 DUF2121: Uncharacterized protein conserved in archaea (DUF2121); InterPro: IPR016754 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=97.18  E-value=0.02  Score=46.31  Aligned_cols=155  Identities=15%  Similarity=0.137  Sum_probs=94.1

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +.+||..+++|+|||.|+|.                      +++-|.-.....|-+.+         ..|.=-+-++|.
T Consensus         2 SLII~y~GknGaViaGDkR~----------------------I~F~G~~~~re~LEeeL---------YsG~IktdeEL~   50 (194)
T PF09894_consen    2 SLIIAYYGKNGAVIAGDKRN----------------------IAFRGDEEKREKLEEEL---------YSGKIKTDEELL   50 (194)
T ss_pred             eEEEEEecCCCcEEecccee----------------------eeecCCHHHHHHHHHHH---------hCCccCCHHHHH
Confidence            57899999999999999972                      45667766655553332         234333445555


Q ss_pred             HHHHHHH---hhccccCCCcceeEEEEEEEEeCC-----CCeEEEEE-------CCCCceecc-------eEEEEeC--C
Q 025640          112 QSLCDTK---QGYTQFGGLRPFGVSFLFAGWDKN-----YGFQLYMS-------DPSGNYGGW-------KAAAIGA--N  167 (250)
Q Consensus       112 ~~l~~~~---~~~~~~~~~rP~~~~~iv~G~d~~-----~~~~Ly~v-------d~~G~~~~~-------~~~a~G~--g  167 (250)
                      +....+=   +-.--+...+-.+- +++|-+-..     ..-.+|..       |-.|+-...       ..+.-|.  -
T Consensus        51 kkA~Elgv~i~I~D~r~KV~~~~~-vlvGEV~s~~g~~skRRRiY~t~g~~~Ivei~~~~i~~~~~g~~sgiIVfGNk~~  129 (194)
T PF09894_consen   51 KKAEELGVKIKITDDREKVRKIGD-VLVGEVTSISGKDSKRRRIYATKGKYAIVEIENDEITNKSRGEGSGIIVFGNKFT  129 (194)
T ss_pred             HHHHHcCCEEEEecCchheEEeCC-EEEEEEEEEcCccceeeEEEecCCCEEEEEecCCeEEEEecCCceeEEEECCHHH
Confidence            5433321   11000111222333 454444221     12356643       222221111       1233332  2


Q ss_pred             hHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeC
Q 025640          168 NQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLM  218 (250)
Q Consensus       168 ~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~  218 (250)
                      .+.+...|.++|++.|+++++.++..++|..+.......+..+++...++.
T Consensus       130 K~ia~~~lkk~~~~k~~l~~i~~i~~~i~~~~a~~tpsvS~~~d~~~~~~~  180 (194)
T PF09894_consen  130 KEIANKELKKYWKPKMSLKDIENIFEKIMEEVASKTPSVSKEYDIYITTKK  180 (194)
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhcCCCccCcEEEEEeccc
Confidence            356888999999999999999999999999998778888999999888654

They do show distant similarity to NTPases and to nucleic acid binding enzymes.

>COG4079 Uncharacterized protein conserved in archaea [Function unknown]

Probab=96.29  E-value=0.11  Score=43.51  Aligned_cols=170  Identities=15%  Similarity=0.175  Sum_probs=108.6

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +.+|+..+++|.|+|.|+|.                      +.+-|.-.|.+.+-+.         +..|.-.+-++|+
T Consensus         2 tLviay~gknGaviaGDrR~----------------------i~frgdee~re~lEek---------LYsGeIkteEEL~   50 (293)
T COG4079           2 TLVIAYIGKNGAVIAGDRRE----------------------ITFRGDEEDREKLEEK---------LYSGEIKTEEELA   50 (293)
T ss_pred             eEEEEEecCCCcEEeccceE----------------------EEEecChhHHHHHHHH---------hhcCccccHHHHH
Confidence            57899999999999999872                      3455666675555333         3355555667777


Q ss_pred             HHHHHHHhhcccc---CCCcceeEEEEEEEEeCCC-----CeEEEEECCCCcee-------c---------ceEEEEeC-
Q 025640          112 QSLCDTKQGYTQF---GGLRPFGVSFLFAGWDKNY-----GFQLYMSDPSGNYG-------G---------WKAAAIGA-  166 (250)
Q Consensus       112 ~~l~~~~~~~~~~---~~~rP~~~~~iv~G~d~~~-----~~~Ly~vd~~G~~~-------~---------~~~~a~G~-  166 (250)
                      +....+--+.+-.   ...|...-.++++-+...+     .-.+|-.  .|++.       +         ...++-|. 
T Consensus        51 r~aeel~Vki~vtDdr~KVrk~~d~VvvGEV~s~~~~~vkRRRvYAT--~Ga~aIvel~gs~vts~~~g~g~aiIv~Gnk  128 (293)
T COG4079          51 RKAEELGVKITVTDDRNKVRKRNDGVVVGEVSSVERGIVKRRRVYAT--AGAYAIVELRGSEVTSTSQGKGSAIIVFGNK  128 (293)
T ss_pred             HHHHHcCCEEEEEcchHhhhcccCcEEEEEeecccccceeeeEEeec--CCceEEEEecCCeeEeeecCCCceEEEECcH
Confidence            7766543222211   1233344456666554421     1244432  23332       0         12334442 


Q ss_pred             -ChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 025640          167 -NNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL  237 (250)
Q Consensus       167 -g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~  237 (250)
                       -.+.++.+|..+|.+.++++++.++..++|..+...-...+..+++..+++.-+   ++.++-.++|+.+.
T Consensus       129 ~~Ke~aneflk~~l~~k~~lqd~~dal~elfe~vss~tpsVskeydiy~vs~~~d---~~~rl~kkDie~L~  197 (293)
T COG4079         129 FTKEVANEFLKDNLTKKSKLQDAVDALMELFETVSSKTPSVSKEYDIYQVSSNVD---PVLRLVKKDIETLR  197 (293)
T ss_pred             HHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHhhcCCCcccceeEEEEecCCcC---HHHHHHHHHHHHHH
Confidence             234588899999999999999999999999999876788999999999986642   24455556665554

>KOG3361 consensus Iron binding protein involved in Fe-S cluster formation [Energy production and conversion]

Probab=81.01  E-value=2.4  Score=32.33  Aligned_cols=44  Identities=23%  Similarity=0.277  Sum_probs=39.9

Q ss_pred             EEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          148 YMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       148 y~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      ..+|-+|-....+|-.-|.|+..+-+-+-..|-.++++|||..+
T Consensus        71 Ikvd~~g~I~dakFKTFGCGSAIASSS~aTewvkgkt~dea~kI  114 (157)
T KOG3361|consen   71 IKVDDSGVIEDAKFKTFGCGSAIASSSLATEWVKGKTLDEALKI  114 (157)
T ss_pred             EEECCCCcEEEeeeeecccchHhhhhHHHHHHHccccHHHHHhc
Confidence            35788999999999999999999999999999999999999764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	250
1z7q_C	258	Crystal Structure Of The 20s Proteasome From Yeast		2e-81
1ryp_C	244	Crystal Structure Of The 20s Proteasome From Yeast		3e-81
1g0u_B	245	A Gated Channel Into The Proteasome Core Particle L		4e-81
3unb_B	261	Mouse Constitutive 20s Proteasome In Complex With P		1e-77
1iru_C	261	Crystal Structure Of The Mammalian 20s Proteasome A		2e-77
3oeu_B	235	Structure Of Yeast 20s Open-Gate Proteasome With Co		5e-76
1vsy_C	232	Proteasome Activator Complex Length = 232		4e-74
3h4p_A	264	Proteasome 20s Core Particle From Methanocaldococcu		6e-50
1j2q_A	237	20s Proteasome In Complex With Calpain-inhibitor I		5e-45
1j2p_A	246	Alpha-Ring From The Proteasome From Archaeoglobus F		1e-44
3jrm_A	227	Crystal Structure Of Archaeal 20s Proteasome In Com		7e-41
1pma_A	233	Proteasome From Thermoplasma Acidophilum Length = 2		8e-41
2ku1_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		9e-41
1yar_A	233	Structure Of Archeabacterial 20s Proteasome Mutant		4e-40
1yau_A	233	Structure Of Archeabacterial 20s Proteasome- Pa26 C		1e-39
2ku2_A	237	Dynamic Regulation Of Archaeal Proteasome Gate Open		2e-39
1iru_B	233	Crystal Structure Of The Mammalian 20s Proteasome A		2e-37
3unb_A	234	Mouse Constitutive 20s Proteasome In Complex With P		2e-37
3une_C	248	Mouse Constitutive 20s Proteasome Length = 248		3e-36
1g0u_D	241	A Gated Channel Into The Proteasome Core Particle L		4e-36
3unb_D	241	Mouse Constitutive 20s Proteasome In Complex With P		5e-36
4g4s_E	261	Structure Of Proteasome-Pba1-Pba2 Complex Length =		1e-35
1fnt_E	260	Crystal Structure Of The 20s Proteasome From Yeast		1e-35
3unb_C	248	Mouse Constitutive 20s Proteasome In Complex With P		1e-35
1vsy_E	250	Proteasome Activator Complex Length = 250		1e-35
2z5c_C	262	Crystal Structure Of A Novel Chaperone Complex For		1e-35
1iru_D	248	Crystal Structure Of The Mammalian 20s Proteasome A		2e-35
1iru_E	241	Crystal Structure Of The Mammalian 20s Proteasome A		4e-35
1ryp_E	242	Crystal Structure Of The 20s Proteasome From Yeast		1e-34
1ryp_D	241	Crystal Structure Of The 20s Proteasome From Yeast		2e-34
1g0u_C	243	A Gated Channel Into The Proteasome Core Particle L		2e-34
1fnt_D	254	Crystal Structure Of The 20s Proteasome From Yeast		2e-34
1iru_A	246	Crystal Structure Of The Mammalian 20s Proteasome A		5e-33
3unb_G	246	Mouse Constitutive 20s Proteasome In Complex With P		8e-33
3unb_F	255	Mouse Constitutive 20s Proteasome In Complex With P		1e-32
1iru_G	254	Crystal Structure Of The Mammalian 20s Proteasome A		1e-32
1g0u_F	248	A Gated Channel Into The Proteasome Core Particle L		2e-32
3oeu_F	242	Structure Of Yeast 20s Open-Gate Proteasome With Co		2e-32
1ryp_G	244	Crystal Structure Of The 20s Proteasome From Yeast		2e-32
1fnt_G	287	Crystal Structure Of The 20s Proteasome From Yeast		2e-32
1z7q_G	288	Crystal Structure Of The 20s Proteasome From Yeast		2e-32
1ryp_B	250	Crystal Structure Of The 20s Proteasome From Yeast		8e-30
1vsy_D	227	Proteasome Activator Complex Length = 227		1e-29
3unb_E	263	Mouse Constitutive 20s Proteasome In Complex With P		2e-26
1g0u_E	234	A Gated Channel Into The Proteasome Core Particle L		2e-26
3sdi_E	233	Structure Of Yeast 20s Open-Gate Proteasome With Co		2e-26
1iru_F	263	Crystal Structure Of The Mammalian 20s Proteasome A		2e-26
1fnt_F	234	Crystal Structure Of The 20s Proteasome From Yeast		6e-26
4g4s_F	235	Structure Of Proteasome-Pba1-Pba2 Complex Length =		6e-26
1ryp_F	233	Crystal Structure Of The 20s Proteasome From Yeast		7e-26
1vsy_B	231	Proteasome Activator Complex Length = 231		1e-24
1g0u_G	252	A Gated Channel Into The Proteasome Core Particle L		8e-23
1ryp_A	243	Crystal Structure Of The 20s Proteasome From Yeast		8e-23
3h4p_a	219	Proteasome 20s Core Particle From Methanocaldococcu		2e-12
1j2q_H	202	20s Proteasome In Complex With Calpain-inhibitor I		1e-11
1ya7_H	217	Implications For Interactions Of Proteasome With Pa		2e-07
1pma_B	211	Proteasome From Thermoplasma Acidophilum Length = 2		2e-07
3c91_H	203	Thermoplasma Acidophilum 20s Proteasome With An Ope		3e-07
3unf_H	234	Mouse 20s Immunoproteasome In Complex With Pr-957 L		1e-05
1iru_K	201	Crystal Structure Of The Mammalian 20s Proteasome A		4e-05
3unb_J	201	Mouse Constitutive 20s Proteasome In Complex With P		4e-05
1g0u_L	241	A Gated Channel Into The Proteasome Core Particle L		4e-04
3unb_N	205	Mouse Constitutive 20s Proteasome In Complex With P		6e-04
1ryp_I	222	Crystal Structure Of The 20s Proteasome From Yeast		8e-04
1fnt_I	232	Crystal Structure Of The 20s Proteasome From Yeast		8e-04
3nzj_H	261	Crystal Structure Of Yeast 20s Proteasome In Comple		9e-04

>pdb|1Z7Q|C Chain C, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 258

Iteration: 1
 Score =  298 bits (763), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 140/244 (57%), Positives = 184/244 (75%), Gaps = 1/244 (0%)
Query: 2   SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
           SRRYDSRTTIFSPEGRLYQVEYA+E+I +AG+AIGI++ DG+VL  E+KVTS LL+  TS
Sbjct: 3   SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 62
Query: 62  TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
           TEK+YK++D +A AVAG+ +DA ILINTAR+ AQ Y   Y E +PVE LV+ L D KQGY
Sbjct: 63  TEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGY 122
Query: 122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKD 181
           TQ GGLRPFGVSF++AG+D  YG+QLY S+PSGNY GWK            ++L+ DYKD
Sbjct: 123 TQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 182
Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPS-GKVKYQVCSPEALSKLLVKH 240
           D+  ++A++LALK LSKT DS++LT D+LE A +    + G+V  ++  P+ +  +LVK 
Sbjct: 183 DMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKT 242
Query: 241 GVTQ 244
           G+T+
Sbjct: 243 GITK 246

>pdb|1RYP|C Chain C, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 244

Iteration: 1
 Score =  297 bits (761), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 140/243 (57%), Positives = 183/243 (75%), Gaps = 1/243 (0%)
Query: 2   SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
           SRRYDSRTTIFSPEGRLYQVEYA+E+I +AG+AIGI++ DG+VL  E+KVTS LL+  TS
Sbjct: 2   SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 61
Query: 62  TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
           TEK+YK++D +A AVAG+ +DA ILINTAR+ AQ Y   Y E +PVE LV+ L D KQGY
Sbjct: 62  TEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGY 121
Query: 122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKD 181
           TQ GGLRPFGVSF++AG+D  YG+QLY S+PSGNY GWK            ++L+ DYKD
Sbjct: 122 TQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 181
Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPS-GKVKYQVCSPEALSKLLVKH 240
           D+  ++A++LALK LSKT DS++LT D+LE A +    + G+V  ++  P+ +  +LVK 
Sbjct: 182 DMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKT 241
Query: 241 GVT 243
           G+T
Sbjct: 242 GIT 244

>pdb|1G0U|B Chain B, A Gated Channel Into The Proteasome Core Particle Length = 245

Iteration: 1
 Score =  297 bits (761), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 140/243 (57%), Positives = 183/243 (75%), Gaps = 1/243 (0%)
Query: 2   SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
           SRRYDSRTTIFSPEGRLYQVEYA+E+I +AG+AIGI++ DG+VL  E+KVTS LL+  TS
Sbjct: 3   SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 62
Query: 62  TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
           TEK+YK++D +A AVAG+ +DA ILINTAR+ AQ Y   Y E +PVE LV+ L D KQGY
Sbjct: 63  TEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGY 122
Query: 122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKD 181
           TQ GGLRPFGVSF++AG+D  YG+QLY S+PSGNY GWK            ++L+ DYKD
Sbjct: 123 TQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 182
Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPS-GKVKYQVCSPEALSKLLVKH 240
           D+  ++A++LALK LSKT DS++LT D+LE A +    + G+V  ++  P+ +  +LVK 
Sbjct: 183 DMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKT 242
Query: 241 GVT 243
           G+T
Sbjct: 243 GIT 245

>pdb|3UNB|B Chain B, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 261

Iteration: 1
 Score =  286 bits (731), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 137/238 (57%), Positives = 177/238 (74%), Gaps = 2/238 (0%)
Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIG+AG+ +GIL+ DGV+L  E++   KLL    
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60
Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
            +EK+YK+++ +AC+VAGI SDAN+L N  R+ AQRY   YQEP+P EQLV +LCD KQ 
Sbjct: 61  FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA 120
Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK 180
           YTQFGG RPFGVS L+ GWDK+YGFQLY SDPSGNYGGWK            S+LKQDYK
Sbjct: 121 YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK 180
Query: 181 D-DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
           + +++ + A+ LA+KVL+KTMD + L+++K+E+A      SGK   +V   + + +L+
Sbjct: 181 EGEMTLKSALALAVKVLNKTMDVSKLSAEKVEIA-TLTRESGKTVIRVLKQKEVEQLI 237

>pdb|1IRU|C Chain C, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 261

Iteration: 1
 Score =  285 bits (729), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 136/238 (57%), Positives = 177/238 (74%), Gaps = 2/238 (0%)
Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIG+AG+ +GIL+ DGV+L  E++   KLL    
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60
Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
            +EK+YK+++ +AC+VAGI SDAN+L N  R+ AQRY   YQEP+P EQLV +LCD KQ 
Sbjct: 61  FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA 120
Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK 180
           YTQFGG RPFGVS L+ GWDK+YGFQLY SDPSGNYGGWK            S+LKQDYK
Sbjct: 121 YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK 180
Query: 181 D-DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
           + +++ + A+ LA+KVL+KTMD + L+++K+E+A      +GK   +V   + + +L+
Sbjct: 181 EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIA-TLTRENGKTVIRVLKQKEVEQLI 237

>pdb|3OEU|B Chain B, Structure Of Yeast 20s Open-Gate Proteasome With Compound 24 Length = 235

Iteration: 1
 Score =  280 bits (716), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 132/235 (56%), Positives = 175/235 (74%), Gaps = 1/235 (0%)
Query: 10  TIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKID 69
           TIFSPEGRLYQVEYA+E+I +AG+AIGI++ DG+VL  E+KVTS LL+  TSTEK+YK++
Sbjct: 1   TIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLN 60
Query: 70  DHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRP 129
           D +A AVAG+ +DA ILINTAR+ AQ Y   Y E +PVE LV+ L D KQGYTQ GGLRP
Sbjct: 61  DKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRP 120
Query: 130 FGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAV 189
           FGVSF++AG+D  YG+QLY S+PSGNY GWK            ++L+ DYKDD+  ++A+
Sbjct: 121 FGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDMKVDDAI 180
Query: 190 QLALKVLSKTMDSTSLTSDKLELAEVFLMPS-GKVKYQVCSPEALSKLLVKHGVT 243
           +LALK LSKT DS++LT D+LE A +    + G+V  ++  P+ +  +LVK G+T
Sbjct: 181 ELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKTGIT 235

>pdb|1VSY|C Chain C, Proteasome Activator Complex Length = 232

Iteration: 1
 Score =  274 bits (700), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 129/232 (55%), Positives = 172/232 (74%), Gaps = 1/232 (0%)
Query: 13  SPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHV 72
           SPEGRLYQVEYA+E+I +AG+AIGI++ DG+VL  E+KVTS LL+  TSTEK+YK++D +
Sbjct: 1   SPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKI 60
Query: 73  ACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGV 132
           A AVAG+ +DA ILINTAR+ AQ Y   Y E +PVE LV+ L D KQGYTQ GGLRPFGV
Sbjct: 61  AVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGV 120
Query: 133 SFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAVQLA 192
           SF++AG+D  YG+QLY S+PSGNY GWK            ++L+ DYKDD+  ++A++LA
Sbjct: 121 SFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDMKVDDAIELA 180
Query: 193 LKVLSKTMDSTSLTSDKLELAEVFLMPS-GKVKYQVCSPEALSKLLVKHGVT 243
           LK LSKT DS++LT D+LE A +    + G+V  ++  P+ +  +LVK G+T
Sbjct: 181 LKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKTGIT 232

>pdb|3H4P|A Chain A, Proteasome 20s Core Particle From Methanocaldococcus Jannaschii Length = 264

Iteration: 1
 Score =  194 bits (492), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 93/194 (47%), Positives = 133/194 (68%), Gaps = 2/194 (1%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSPEGRLYQVEYA EA+    +AIGI  KDGVVL  ++++TSKL++   S EK
Sbjct: 12  YDRAITVFSPEGRLYQVEYAREAVRRGTTAIGIACKDGVVLAVDRRITSKLVKIR-SIEK 70
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +++IDDHVA A +G+++DA +LI+ AR++AQ Y   Y E + +E L + +CD KQ YTQ 
Sbjct: 71  IFQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQH 130
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDIS 184
           GG+RPFGVS L AG DKN   +L+ +DPSG    +K             +L+++Y+DDI+
Sbjct: 131 GGVRPFGVSLLIAGIDKNEA-RLFETDPSGALIEYKATAIGSGRPVVMELLEKEYRDDIT 189
Query: 185 REEAVQLALKVLSK 198
            +E ++LA+  L+K
Sbjct: 190 LDEGLELAITALTK 203

>pdb|1J2Q|A Chain A, 20s Proteasome In Complex With Calpain-inhibitor I From Archaeoglobus Fulgidus Length = 237

Iteration: 1
 Score =  177 bits (449), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 88/206 (42%), Positives = 136/206 (66%), Gaps = 4/206 (1%)
Query: 10  TIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKID 69
           T+FSP+GRL+QVEYA EA+    +AIGI  K+GV+L+ +K+V SKLL+  T  EK+YKID
Sbjct: 4   TVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEADT-IEKIYKID 62
Query: 70  DHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRP 129
           +H+  A +G+++DA +LI+ AR++AQ     Y EP+ V++L + +CD KQ YTQ+GG+RP
Sbjct: 63  EHICAATSGLVADARVLIDRARIEAQINRLTYDEPITVKELAKKICDFKQQYTQYGGVRP 122
Query: 130 FGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAV 189
           FGVS L AG D+    +LY +DPSG    +K               +++Y+DD+S ++A+
Sbjct: 123 FGVSLLIAGVDEVP--KLYETDPSGALLEYKATAIGMGRNAVTEFFEKEYRDDLSFDDAM 180
Query: 190 QLALKVLSKTMDSTSLTSDKLELAEV 215
            L L  +  +++S  L  + +E+  V
Sbjct: 181 VLGLVAMGLSIES-ELVPENIEVGYV 205

>pdb|1J2P|A Chain A, Alpha-Ring From The Proteasome From Archaeoglobus Fulgidus Length = 246

Iteration: 1
 Score =  176 bits (446), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 89/211 (42%), Positives = 136/211 (64%), Gaps = 4/211 (1%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+GRL+QVEYA EA+    +AIGI  K+GV+L+ +K+V SKLL+  T  EK
Sbjct: 8   YDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEKDT-IEK 66
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +YKID+H+  A +G+++DA +LI+ AR++AQ     Y  P+ V++L + +CD KQ YTQ+
Sbjct: 67  IYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQY 126
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDIS 184
           GG+RPFGVS L AG   N   +LY +DPSG    +K               +++Y+DD+S
Sbjct: 127 GGVRPFGVSLLIAGV--NEVPKLYETDPSGALLEYKATAIGMGRMAVTEFFEKEYRDDLS 184
Query: 185 REEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
            ++A+ L L  +  +++S  L  + +E+  V
Sbjct: 185 FDDAMVLGLVAMGLSIES-ELVPENIEVGYV 214

>pdb|3JRM|A Chain A, Crystal Structure Of Archaeal 20s Proteasome In Complex With Mutated P26 Activator Length = 227

Iteration: 1
 Score =  163 bits (413), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 86/233 (36%), Positives = 144/233 (61%), Gaps = 7/233 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+GRL+QVEYA EA+    +A+G+   +GV+L+ +KKV S+L++ + S EK
Sbjct: 2   YDRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEK 60
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  IDD+VA   +G+++DA +L++ AR+ AQ+    Y   + +E LV+ + D  Q YTQ+
Sbjct: 61  IQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQY 120
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDIS 184
           GG+RP+GVS +FAG D+  G +L+  DP+G    +K            S L+++YK+++ 
Sbjct: 121 GGVRPYGVSLIFAGIDQ-IGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLP 179
Query: 185 REEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            +EAV L +K L  +++      ++L+  E+  +  G  KY++   E + K L
Sbjct: 180 EKEAVTLGIKALKSSLEE----GEELKAPEIASITVGN-KYRIYDQEEVKKFL 227

>pdb|1PMA|A Chain A, Proteasome From Thermoplasma Acidophilum Length = 233

Iteration: 1
 Score =  163 bits (413), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 86/233 (36%), Positives = 144/233 (61%), Gaps = 7/233 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+GRL+QVEYA EA+    +A+G+   +GV+L+ +KKV S+L++ + S EK
Sbjct: 8   YDRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEK 66
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  IDD+VA   +G+++DA +L++ AR+ AQ+    Y   + +E LV+ + D  Q YTQ+
Sbjct: 67  IQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQY 126
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDIS 184
           GG+RP+GVS +FAG D+  G +L+  DP+G    +K            S L+++YK+++ 
Sbjct: 127 GGVRPYGVSLIFAGIDQ-IGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLP 185
Query: 185 REEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            +EAV L +K L  +++      ++L+  E+  +  G  KY++   E + K L
Sbjct: 186 EKEAVTLGIKALKSSLEE----GEELKAPEIASITVGN-KYRIYDQEEVKKFL 233

>pdb|2KU1|A Chain A, Dynamic Regulation Of Archaeal Proteasome Gate Opening As Studied By Trosy-Nmr Length = 237

Iteration: 1
 Score =  163 bits (412), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 86/233 (36%), Positives = 144/233 (61%), Gaps = 7/233 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+GRL+QVEYA EA+    +A+G+   +GV+L+ +KKV S+L++ + S EK
Sbjct: 12  YDRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEK 70
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  IDD+VA   +G+++DA +L++ AR+ AQ+    Y   + +E LV+ + D  Q YTQ+
Sbjct: 71  IQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQY 130
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDIS 184
           GG+RP+GVS +FAG D+  G +L+  DP+G    +K            S L+++YK+++ 
Sbjct: 131 GGVRPYGVSLIFAGIDQ-IGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLP 189
Query: 185 REEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            +EAV L +K L  +++      ++L+  E+  +  G  KY++   E + K L
Sbjct: 190 EKEAVTLGIKALKSSLEE----GEELKAPEIASITVGN-KYRIYDQEEVKKFL 237

>pdb|1YAR|A Chain A, Structure Of Archeabacterial 20s Proteasome Mutant D9s- Pa26 Complex Length = 233

Iteration: 1
 Score =  160 bits (406), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 85/233 (36%), Positives = 143/233 (61%), Gaps = 7/233 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           Y    T+FSP+GRL+QVEYA EA+    +A+G+   +GV+L+ +KKV S+L++ + S EK
Sbjct: 8   YSRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEK 66
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  IDD+VA   +G+++DA +L++ AR+ AQ+    Y   + +E LV+ + D  Q YTQ+
Sbjct: 67  IQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQY 126
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDIS 184
           GG+RP+GVS +FAG D+  G +L+  DP+G    +K            S L+++YK+++ 
Sbjct: 127 GGVRPYGVSLIFAGIDQ-IGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLP 185
Query: 185 REEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            +EAV L +K L  +++      ++L+  E+  +  G  KY++   E + K L
Sbjct: 186 EKEAVTLGIKALKSSLEE----GEELKAPEIASITVGN-KYRIYDQEEVKKFL 233

>pdb|1YAU|A Chain A, Structure Of Archeabacterial 20s Proteasome- Pa26 Complex Length = 233

Iteration: 1
 Score =  159 bits (403), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 142/228 (62%), Gaps = 7/228 (3%)
Query: 10  TIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKID 69
           T+FSP+GRL+QVEYA EA+    +A+G+   +GV+L+ +KKV S+L++ + S EK+  ID
Sbjct: 13  TVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEKIQLID 71
Query: 70  DHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRP 129
           D+VA   +G+++DA +L++ AR+ AQ+    Y   + +E LV+ + D  Q YTQ+GG+RP
Sbjct: 72  DYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRP 131
Query: 130 FGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAV 189
           +GVS +FAG D+  G +L+  DP+G    +K            S L+++YK+++  +EAV
Sbjct: 132 YGVSLIFAGIDQ-IGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLPEKEAV 190
Query: 190 QLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            L +K L  +++      ++L+  E+  +  G  KY++   E + K L
Sbjct: 191 TLGIKALKSSLEE----GEELKAPEIASITVGN-KYRIYDQEEVKKFL 233

>pdb|2KU2|A Chain A, Dynamic Regulation Of Archaeal Proteasome Gate Opening As Studied By Trosy-Nmr Length = 237

Iteration: 1
 Score =  159 bits (402), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 142/228 (62%), Gaps = 7/228 (3%)
Query: 10  TIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKID 69
           T+FSP+GRL+QVEYA EA+    +A+G+   +GV+L+ +KKV S+L++ + S EK+  ID
Sbjct: 17  TVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIEQN-SIEKIQLID 75
Query: 70  DHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRP 129
           D+VA   +G+++DA +L++ AR+ AQ+    Y   + +E LV+ + D  Q YTQ+GG+RP
Sbjct: 76  DYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRP 135
Query: 130 FGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAV 189
           +GVS +FAG D+  G +L+  DP+G    +K            S L+++YK+++  +EAV
Sbjct: 136 YGVSLIFAGIDQ-IGPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLPEKEAV 194
Query: 190 QLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            L +K L  +++      ++L+  E+  +  G  KY++   E + K L
Sbjct: 195 TLGIKALKSSLEE----GEELKAPEIASITVGN-KYRIYDQEEVKKFL 237

>pdb|1IRU|B Chain B, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 233

Iteration: 1
 Score =  152 bits (383), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 79/210 (37%), Positives = 117/210 (55%), Gaps = 3/210 (1%)
Query: 3   RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTST 62
           R Y    T FSP G+L Q+EYA+ A+     ++GI + +GVVL  EKK  S +L    S 
Sbjct: 3   RGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKS-ILYDERSV 61
Query: 63  EKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYT 122
            K+  I  H+    +G+  D  +L++ AR  AQ+Y   YQEP+P  QLVQ +    Q YT
Sbjct: 62  HKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYT 121
Query: 123 QFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDD 182
           Q GG+RPFGVS L  GW++   + L+ SDPSG Y  WK            + L++ Y +D
Sbjct: 122 QSGGVRPFGVSLLICGWNEGRPY-LFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNED 180
Query: 183 ISREEAVQLALKVLSKTMDSTSLTSDKLEL 212
           +  E+A+  A+  L ++ +   +T D +E+
Sbjct: 181 LELEDAIHTAILTLKESFEG-QMTEDNIEV 209

>pdb|3UNB|A Chain A, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 234

Iteration: 1
 Score =  152 bits (383), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 79/210 (37%), Positives = 117/210 (55%), Gaps = 3/210 (1%)
Query: 3   RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTST 62
           R Y    T FSP G+L Q+EYA+ A+     ++GI + +GVVL  EKK  S +L    S 
Sbjct: 4   RGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKS-ILYDERSV 62
Query: 63  EKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYT 122
            K+  I  H+    +G+  D  +L++ AR  AQ+Y   YQEP+P  QLVQ +    Q YT
Sbjct: 63  HKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYT 122
Query: 123 QFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDD 182
           Q GG+RPFGVS L  GW++   + L+ SDPSG Y  WK            + L++ Y +D
Sbjct: 123 QSGGVRPFGVSLLICGWNEGRPY-LFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNED 181
Query: 183 ISREEAVQLALKVLSKTMDSTSLTSDKLEL 212
           +  E+A+  A+  L ++ +   +T D +E+
Sbjct: 182 LELEDAIHTAILTLKESFEG-QMTEDNIEV 210

>pdb|3UNE|C Chain C, Mouse Constitutive 20s Proteasome Length = 248

Iteration: 1
 Score =  148 bits (374), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 78/200 (39%), Positives = 116/200 (58%), Gaps = 3/200 (1%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+G L+QVEYA EA+    +A+G+  KD VVL  EKK  +KL Q   +  K
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGKDIVVLGVEKKSVAKL-QDERTVRK 61
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +DD+V  A AG+ +DA I+IN ARV+ Q +    ++P+ VE + + +   KQ YTQ 
Sbjct: 62  ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQS 121
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDI- 183
            G RPFG+S L  G+D +   +LY +DPSG Y  WK              L+++Y DD  
Sbjct: 122 NGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDDAI 181
Query: 184 -SREEAVQLALKVLSKTMDS 202
            + +  ++L +K L + + S
Sbjct: 182 ETDDLTIKLVIKALLEVVQS 201

>pdb|1G0U|D Chain D, A Gated Channel Into The Proteasome Core Particle Length = 241

Iteration: 1
 Score =  147 bits (372), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 79/198 (39%), Positives = 116/198 (58%), Gaps = 4/198 (2%)
Query: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
            YD   + FSPEGRL+QVEY++EAI    +AIGI +K+GVVL  EK+ TS LL+ S S E
Sbjct: 7   EYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIE 65
Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
           K+ +ID H+ CA++G+ +DA  +I  AR  A  +   Y E + VE L QS+CD       
Sbjct: 66  KIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLAAAAAM 125
Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDI 183
               RPFGV+ L AG D + G+QL+ ++PSG +  +             + L  ++   +
Sbjct: 126 S---RPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWHSSL 182
Query: 184 SREEAVQLALKVLSKTMD 201
           + +EA  L LK+L + M+
Sbjct: 183 TLKEAELLVLKILKQVME 200

>pdb|3UNB|D Chain D, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 241

Iteration: 1
 Score =  147 bits (371), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 85/220 (38%), Positives = 127/220 (57%), Gaps = 14/220 (6%)
Query: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
            YD     FSPEGRL+QVEYA+EAI    +AIGI + +GV L  EK++TS L++ S S E
Sbjct: 7   EYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPS-SIE 65
Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
           K+ +ID H+ CA++G+++DA  LI+ ARV+ Q + + Y E M VE + Q++ +      Q
Sbjct: 66  KIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA---LQ 122
Query: 124 FGG--------LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSIL 175
           FG          RPFGV+ LF G D+  G QL+  DPSG +                S L
Sbjct: 123 FGEEDADPGAMSRPFGVALLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSASEGAQSSL 181
Query: 176 KQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
           ++ Y   ++ +EA++ +L +L + M+   L +  +ELA V
Sbjct: 182 QEVYHKSMTLKEAIKSSLIILKQVMEE-KLNATNIELATV 220

>pdb|4G4S|E Chain E, Structure Of Proteasome-Pba1-Pba2 Complex Length = 261

Iteration: 1
 Score =  145 bits (367), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 79/203 (38%), Positives = 118/203 (58%), Gaps = 7/203 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   + FSPEGRL+QVEY++EAI    +AIGI +K+GVVL  EK+ TS LL+ S S EK
Sbjct: 9   YDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEK 67
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + +ID H+ CA++G+ +DA  +I  AR  A  +   Y E + VE L QS+CD    + + 
Sbjct: 68  IVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEG 127
Query: 125 GG------LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQD 178
                    RPFGV+ L AG D + G+QL+ ++PSG +  +             + L  +
Sbjct: 128 ASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNE 187
Query: 179 YKDDISREEAVQLALKVLSKTMD 201
           +   ++ +EA  L LK+L + M+
Sbjct: 188 WHSSLTLKEAELLVLKILKQVME 210

>pdb|1FNT|E Chain E, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 260

Iteration: 1
 Score =  145 bits (367), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 79/203 (38%), Positives = 118/203 (58%), Gaps = 7/203 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   + FSPEGRL+QVEY++EAI    +AIGI +K+GVVL  EK+ TS LL+ S S EK
Sbjct: 8   YDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEK 66
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + +ID H+ CA++G+ +DA  +I  AR  A  +   Y E + VE L QS+CD    + + 
Sbjct: 67  IVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEG 126
Query: 125 GG------LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQD 178
                    RPFGV+ L AG D + G+QL+ ++PSG +  +             + L  +
Sbjct: 127 ASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNE 186
Query: 179 YKDDISREEAVQLALKVLSKTMD 201
           +   ++ +EA  L LK+L + M+
Sbjct: 187 WHSSLTLKEAELLVLKILKQVME 209

>pdb|3UNB|C Chain C, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 248

Iteration: 1
 Score =  145 bits (367), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 77/200 (38%), Positives = 115/200 (57%), Gaps = 3/200 (1%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+G L+QVEYA EA+    +A+G+  KD VVL   KK  +KL Q   +  K
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGKDIVVLGVAKKSVAKL-QDERTVRK 61
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +DD+V  A AG+ +DA I+IN ARV+ Q +    ++P+ VE + + +   KQ YTQ 
Sbjct: 62  ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQS 121
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDI- 183
            G RPFG+S L  G+D +   +LY +DPSG Y  WK              L+++Y DD  
Sbjct: 122 NGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDDAI 181
Query: 184 -SREEAVQLALKVLSKTMDS 202
            + +  ++L +K L + + S
Sbjct: 182 ETDDLTIKLVIKALLEVVQS 201

>pdb|1VSY|E Chain E, Proteasome Activator Complex Length = 250

Iteration: 1
 Score =  145 bits (367), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 79/203 (38%), Positives = 118/203 (58%), Gaps = 7/203 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   + FSPEGRL+QVEY++EAI    +AIGI +K+GVVL  EK+ TS LL+ S S EK
Sbjct: 8   YDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEK 66
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + +ID H+ CA++G+ +DA  +I  AR  A  +   Y E + VE L QS+CD    + + 
Sbjct: 67  IVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEG 126
Query: 125 GG------LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQD 178
                    RPFGV+ L AG D + G+QL+ ++PSG +  +             + L  +
Sbjct: 127 ASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNE 186
Query: 179 YKDDISREEAVQLALKVLSKTMD 201
           +   ++ +EA  L LK+L + M+
Sbjct: 187 WHSSLTLKEAELLVLKILKQVME 209

>pdb|2Z5C|C Chain C, Crystal Structure Of A Novel Chaperone Complex For Yeast 20s Proteasome Assembly Length = 262

Iteration: 1
 Score =  145 bits (367), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 79/203 (38%), Positives = 118/203 (58%), Gaps = 7/203 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   + FSPEGRL+QVEY++EAI    +AIGI +K+GVVL  EK+ TS LL+ S S EK
Sbjct: 10  YDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEK 68
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + +ID H+ CA++G+ +DA  +I  AR  A  +   Y E + VE L QS+CD    + + 
Sbjct: 69  IVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEG 128
Query: 125 GG------LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQD 178
                    RPFGV+ L AG D + G+QL+ ++PSG +  +             + L  +
Sbjct: 129 ASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNE 188
Query: 179 YKDDISREEAVQLALKVLSKTMD 201
           +   ++ +EA  L LK+L + M+
Sbjct: 189 WHSSLTLKEAELLVLKILKQVME 211

>pdb|1IRU|D Chain D, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 248

Iteration: 1
 Score =  145 bits (367), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 76/200 (38%), Positives = 116/200 (58%), Gaps = 3/200 (1%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+G L+QVEYA EA+    +A+G+  +D VVL  EKK  +KL Q   +  K
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKL-QDERTVRK 61
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +DD+V  A AG+ +DA I+IN ARV+ Q +    ++P+ VE + + +   KQ YTQ 
Sbjct: 62  ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQS 121
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDI- 183
            G RPFG+S L  G+D +   +LY +DPSG Y  WK              L+++Y D+  
Sbjct: 122 NGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAI 181
Query: 184 -SREEAVQLALKVLSKTMDS 202
            + +  ++L +K L + + S
Sbjct: 182 ETDDLTIKLVIKALLEVVQS 201

>pdb|1IRU|E Chain E, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 241

Iteration: 1
 Score =  144 bits (364), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 84/220 (38%), Positives = 126/220 (57%), Gaps = 14/220 (6%)
Query: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
            YD     FSPEGRL+QVEY +EAI    +AIGI + +GV L  EK++TS L++ S S E
Sbjct: 7   EYDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPS-SIE 65
Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
           K+ +ID H+ CA++G+++DA  LI+ ARV+ Q + + Y E M VE + Q++ +      Q
Sbjct: 66  KIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA---LQ 122
Query: 124 FGG--------LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSIL 175
           FG          RPFGV+ LF G D+  G QL+  DPSG +                S L
Sbjct: 123 FGEEDADPGAMSRPFGVALLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSASEGAQSSL 181
Query: 176 KQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
           ++ Y   ++ +EA++ +L +L + M+   L +  +ELA V
Sbjct: 182 QELYHKSMTLKEAIKSSLIILKQVMEE-KLNATNIELATV 220

>pdb|1RYP|E Chain E, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 242

Iteration: 1
 Score =  143 bits (360), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 78/202 (38%), Positives = 117/202 (57%), Gaps = 7/202 (3%)
Query: 6   DSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKM 65
           D   + FSPEGRL+QVEY++EAI    +AIGI +K+GVVL  EK+ TS LL+ S S EK+
Sbjct: 1   DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEKI 59
Query: 66  YKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFG 125
            +ID H+ CA++G+ +DA  +I  AR  A  +   Y E + VE L QS+CD    + +  
Sbjct: 60  VEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGA 119
Query: 126 G------LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDY 179
                   RPFGV+ L AG D + G+QL+ ++PSG +  +             + L  ++
Sbjct: 120 SGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEW 179
Query: 180 KDDISREEAVQLALKVLSKTMD 201
              ++ +EA  L LK+L + M+
Sbjct: 180 HSSLTLKEAELLVLKILKQVME 201

>pdb|1RYP|D Chain D, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 241

Iteration: 1
 Score =  142 bits (357), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 75/196 (38%), Positives = 116/196 (59%), Gaps = 4/196 (2%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   +IFSP+G ++QVEYA+EA+     A+G+  K+ VVL  E++ T KL  T  +  K
Sbjct: 2   YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 61
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + KID HV  + +G+ +D+ ILI  ARV+AQ +    ++P+ VE L + +   +Q YTQ 
Sbjct: 62  VSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQS 121
Query: 125 GGLRPFGVSFLFAGWD-KNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDY---K 180
           GG+RPFGVS L AG+D ++   +LY ++PSG Y  W               L+++Y   +
Sbjct: 122 GGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKE 181
Query: 181 DDISREEAVQLALKVL 196
              + EE V+L ++ L
Sbjct: 182 PPATVEECVKLTVRSL 197

>pdb|1G0U|C Chain C, A Gated Channel Into The Proteasome Core Particle Length = 243

Iteration: 1
 Score =  142 bits (357), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 75/196 (38%), Positives = 116/196 (59%), Gaps = 4/196 (2%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   +IFSP+G ++QVEYA+EA+     A+G+  K+ VVL  E++ T KL  T  +  K
Sbjct: 4   YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 63
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + KID HV  + +G+ +D+ ILI  ARV+AQ +    ++P+ VE L + +   +Q YTQ 
Sbjct: 64  VSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQS 123
Query: 125 GGLRPFGVSFLFAGWD-KNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDY---K 180
           GG+RPFGVS L AG+D ++   +LY ++PSG Y  W               L+++Y   +
Sbjct: 124 GGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKE 183
Query: 181 DDISREEAVQLALKVL 196
              + EE V+L ++ L
Sbjct: 184 PPATVEECVKLTVRSL 199

>pdb|1FNT|D Chain D, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 254

Iteration: 1
 Score =  142 bits (357), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 75/196 (38%), Positives = 116/196 (59%), Gaps = 4/196 (2%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   +IFSP+G ++QVEYA+EA+     A+G+  K+ VVL  E++ T KL  T  +  K
Sbjct: 4   YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 63
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + KID HV  + +G+ +D+ ILI  ARV+AQ +    ++P+ VE L + +   +Q YTQ 
Sbjct: 64  VSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQS 123
Query: 125 GGLRPFGVSFLFAGWD-KNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDY---K 180
           GG+RPFGVS L AG+D ++   +LY ++PSG Y  W               L+++Y   +
Sbjct: 124 GGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKE 183
Query: 181 DDISREEAVQLALKVL 196
              + EE V+L ++ L
Sbjct: 184 PPATVEECVKLTVRSL 199

>pdb|1IRU|A Chain A, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 246

Iteration: 1
 Score =  137 bits (346), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 73/199 (36%), Positives = 111/199 (55%), Gaps = 4/199 (2%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAG-SAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
           +D   TIFSPEGRLYQVEYA +AI   G +++ +  KD  V+V +KKV  KLL +ST T 
Sbjct: 9   FDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTH 68
Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
            ++KI +++ C + G+ +D+   +  AR +A  + Y Y   +PV+ L + + D  Q YTQ
Sbjct: 69  -LFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQ 127
Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKD-- 181
              +RP G   +  G D+  G Q+Y  DP+G Y G+K            S L++  K   
Sbjct: 128 NAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKF 187
Query: 182 DISREEAVQLALKVLSKTM 200
           D + E+ V+ A+  LS  +
Sbjct: 188 DWTFEQTVETAITCLSTVL 206

>pdb|3UNB|G Chain G, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 246

Iteration: 1
 Score =  137 bits (344), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 73/199 (36%), Positives = 110/199 (55%), Gaps = 4/199 (2%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAG-SAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
           +D   TIFSPEGRLYQVEYA +AI   G +++ +  KD  V+V +KKV  KLL +ST T 
Sbjct: 9   FDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTH 68
Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
            ++KI + + C + G+ +D+   +  AR +A  + Y Y   +PV+ L + + D  Q YTQ
Sbjct: 69  -LFKITESIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQ 127
Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKD-- 181
              +RP G   +  G D+  G Q+Y  DP+G Y G+K            S L++  K   
Sbjct: 128 NAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKF 187
Query: 182 DISREEAVQLALKVLSKTM 200
           D + E+ V+ A+  LS  +
Sbjct: 188 DWTFEQTVETAITCLSTVL 206

>pdb|3UNB|F Chain F, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 255

Iteration: 1
 Score =  136 bits (343), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 79/219 (36%), Positives = 120/219 (54%), Gaps = 3/219 (1%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   + FSP+GR++QVEYAM+A+ N+ +AIGI  KDGVV   EK V SKL +   S ++
Sbjct: 8   YDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEG-SNKR 66
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           ++ +D HV  AVAG+++DA  L + AR +A  +   +   +P++ L   +      YT +
Sbjct: 67  LFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLY 126
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSG-NYGGWKXXXXXXXXXXXXSILKQDYKDDI 183
             +RPFG SF+   +  N G QLYM DPSG +YG W              I K   K+  
Sbjct: 127 SAVRPFGCSFMLGSYSANDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMT 186
Query: 184 SREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGK 222
            R+   ++A K++    D     + +LEL+ V  +  G+
Sbjct: 187 CRDVVKEVA-KIIYIVHDEVKDKAFELELSWVGELTKGR 224

>pdb|1IRU|G Chain G, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 254

Iteration: 1
 Score =  135 bits (341), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 79/219 (36%), Positives = 121/219 (55%), Gaps = 3/219 (1%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   + FSP+GR++QVEYAM+A+ N+ +AIGI  KDGVV   EK V SKL +   S ++
Sbjct: 7   YDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEG-SNKR 65
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           ++ +D HV  AVAG+++DA  L + AR +A  +   +   +P++ L   +      YT +
Sbjct: 66  LFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLY 125
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSG-NYGGWKXXXXXXXXXXXXSILKQDYKDDI 183
             +RPFG SF+   +  N G QLYM DPSG +YG W              I K   K+  
Sbjct: 126 SAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMT 185
Query: 184 SREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGK 222
            R+   ++A K++    D     + +LEL+ V  + +G+
Sbjct: 186 CRDIVKEVA-KIIYIVHDEVKDKAFELELSWVGELTNGR 223

>pdb|1G0U|F Chain F, A Gated Channel Into The Proteasome Core Particle Length = 248

Iteration: 1
 Score =  135 bits (341), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 74/212 (34%), Positives = 117/212 (55%), Gaps = 5/212 (2%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   ++FSP+GR +QVEYA++A+ N  ++IGI   DGVV   EK +TSKLL    +  K
Sbjct: 8   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV-K 66
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +D H+ C  +G++ D   L+N  R +A  +   Y+ P+P+      L    Q +T +
Sbjct: 67  IQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLY 126
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQ---DYKD 181
             +RPFGVS +F G DKN G  LYM +PSG+Y G+K            + L++    + +
Sbjct: 127 NSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPE 185
Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELA 213
            +S  EAV+ A K++    +       +LE++
Sbjct: 186 GLSAREAVKQAAKIIYLAHEDNKEKDFELEIS 217

>pdb|3OEU|F Chain F, Structure Of Yeast 20s Open-Gate Proteasome With Compound 24 Length = 242

Iteration: 1
 Score =  135 bits (341), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 74/212 (34%), Positives = 117/212 (55%), Gaps = 5/212 (2%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   ++FSP+GR +QVEYA++A+ N  ++IGI   DGVV   EK +TSKLL    +  K
Sbjct: 2   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV-K 60
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +D H+ C  +G++ D   L+N  R +A  +   Y+ P+P+      L    Q +T +
Sbjct: 61  IQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLY 120
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQ---DYKD 181
             +RPFGVS +F G DKN G  LYM +PSG+Y G+K            + L++    + +
Sbjct: 121 NSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPE 179
Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELA 213
            +S  EAV+ A K++    +       +LE++
Sbjct: 180 GLSAREAVKQAAKIIYLAHEDNKEKDFELEIS 211

>pdb|1RYP|G Chain G, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 244

Iteration: 1
 Score =  135 bits (340), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 74/212 (34%), Positives = 117/212 (55%), Gaps = 5/212 (2%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   ++FSP+GR +QVEYA++A+ N  ++IGI   DGVV   EK +TSKLL    +  K
Sbjct: 4   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV-K 62
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +D H+ C  +G++ D   L+N  R +A  +   Y+ P+P+      L    Q +T +
Sbjct: 63  IQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLY 122
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQ---DYKD 181
             +RPFGVS +F G DKN G  LYM +PSG+Y G+K            + L++    + +
Sbjct: 123 NSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPE 181
Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELA 213
            +S  EAV+ A K++    +       +LE++
Sbjct: 182 GLSAREAVKQAAKIIYLAHEDNKEKDFELEIS 213

>pdb|1FNT|G Chain G, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 287

Iteration: 1
 Score =  135 bits (340), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 74/212 (34%), Positives = 117/212 (55%), Gaps = 5/212 (2%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   ++FSP+GR +QVEYA++A+ N  ++IGI   DGVV   EK +TSKLL    +  K
Sbjct: 7   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV-K 65
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +D H+ C  +G++ D   L+N  R +A  +   Y+ P+P+      L    Q +T +
Sbjct: 66  IQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLY 125
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQ---DYKD 181
             +RPFGVS +F G DKN G  LYM +PSG+Y G+K            + L++    + +
Sbjct: 126 NSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPE 184
Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELA 213
            +S  EAV+ A K++    +       +LE++
Sbjct: 185 GLSAREAVKQAAKIIYLAHEDNKEKDFELEIS 216

>pdb|1Z7Q|G Chain G, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 288

Iteration: 1
 Score =  135 bits (340), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 74/212 (34%), Positives = 117/212 (55%), Gaps = 5/212 (2%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   ++FSP+GR +QVEYA++A+ N  ++IGI   DGVV   EK +TSKLL    +  K
Sbjct: 8   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNV-K 66
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +D H+ C  +G++ D   L+N  R +A  +   Y+ P+P+      L    Q +T +
Sbjct: 67  IQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLY 126
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQ---DYKD 181
             +RPFGVS +F G DKN G  LYM +PSG+Y G+K            + L++    + +
Sbjct: 127 NSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPE 185
Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELA 213
            +S  EAV+ A K++    +       +LE++
Sbjct: 186 GLSAREAVKQAAKIIYLAHEDNKEKDFELEIS 217

>pdb|1RYP|B Chain B, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 250

Iteration: 1
 Score =  127 bits (318), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 73/214 (34%), Positives = 116/214 (54%), Gaps = 3/214 (1%)
Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           M+ RY    T FSP G+L Q++YA+ A+    +++GI + +GVV+  EKK +S L  + T
Sbjct: 1   MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET 60
Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTAR-VQAQRYTYAYQEPMPVEQLVQSLCDTKQ 119
            + K+  +   +    +G+  D  +L++ +R V    Y   Y E  P + LV  +    Q
Sbjct: 61  LS-KVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQ 119
Query: 120 GYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDY 179
             TQ GG+RPFGVS L AG D+  GF LY  DPSG+Y  WK            + L++ +
Sbjct: 120 EATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRW 179
Query: 180 KDDISREEAVQLALKVLSKTMDSTSLTSDKLELA 213
            D++  E+A+ +AL  L ++++      D +ELA
Sbjct: 180 NDELELEDAIHIALLTLKESVEG-EFNGDTIELA 212

>pdb|1VSY|D Chain D, Proteasome Activator Complex Length = 227

Iteration: 1
 Score =  126 bits (317), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 68/183 (37%), Positives = 107/183 (58%), Gaps = 4/183 (2%)
Query: 18  LYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVA 77
           ++QVEYA+EA+     A+G+  K+ VVL  E++ T KL  T  +  K+ KID HV  + +
Sbjct: 1   IFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFS 60
Query: 78  GIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFA 137
           G+ +D+ ILI  ARV+AQ +    ++P+ VE L + +   +Q YTQ GG+RPFGVS L A
Sbjct: 61  GLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIA 120
Query: 138 GWD-KNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDY---KDDISREEAVQLAL 193
           G+D ++   +LY ++PSG Y  W               L+++Y   +   + EE V+L +
Sbjct: 121 GFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTV 180
Query: 194 KVL 196
           + L
Sbjct: 181 RSL 183

>pdb|3UNB|E Chain E, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 263

Iteration: 1
 Score =  115 bits (289), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 61/199 (30%), Positives = 110/199 (55%), Gaps = 6/199 (3%)
Query: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
           +YD+  T++SP+GR++Q+EYAMEA+    + +G+ SK   VLV  K+  S+L   +   +
Sbjct: 5   QYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSEL---AAHQK 61
Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
           K+  +D+H+  ++AG+ +DA +L N  R +     + +  P+PV +LV  +    Q  TQ
Sbjct: 62  KILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQ 121
Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKD-- 181
             G RP+GV  L AG+D + G  ++ + PS NY   +            + L++   +  
Sbjct: 122 RYGRRPYGVGLLIAGYD-DMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM 180
Query: 182 DISREEAVQLALKVLSKTM 200
           + + +E V+  L+ L +T+
Sbjct: 181 ECNLDELVKHGLRALRETL 199

>pdb|1G0U|E Chain E, A Gated Channel Into The Proteasome Core Particle Length = 234

Iteration: 1
 Score =  115 bits (288), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 74/215 (34%), Positives = 107/215 (49%), Gaps = 8/215 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD  T  FSP GRL+QVEYA+EAI      +G+ S    VLV  K+   +L   S+  +K
Sbjct: 6   YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL---SSYQKK 62
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + K D+H+  ++AG+  DA +L N  R Q    +  +   + VE+    LCD  Q  TQ 
Sbjct: 63  IIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQS 122
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGN----YGGWKXXXXXXXXXXXXSILKQDYK 180
            G RP+GV  L  G+DK+ G  L    PSGN    YG                 L    K
Sbjct: 123 AGGRPYGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIK 181
Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
            D + +E ++  ++ +S+++   SLT D L +A V
Sbjct: 182 IDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIV 216

>pdb|3SDI|E Chain E, Structure Of Yeast 20s Open-Gate Proteasome With Compound 20 Length = 233

Iteration: 1
 Score =  115 bits (288), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 74/215 (34%), Positives = 107/215 (49%), Gaps = 8/215 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD  T  FSP GRL+QVEYA+EAI      +G+ S    VLV  K+   +L   S+  +K
Sbjct: 5   YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL---SSYQKK 61
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + K D+H+  ++AG+  DA +L N  R Q    +  +   + VE+    LCD  Q  TQ 
Sbjct: 62  IIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQS 121
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGN----YGGWKXXXXXXXXXXXXSILKQDYK 180
            G RP+GV  L  G+DK+ G  L    PSGN    YG                 L    K
Sbjct: 122 AGGRPYGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIK 180
Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
            D + +E ++  ++ +S+++   SLT D L +A V
Sbjct: 181 IDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIV 215

>pdb|1IRU|F Chain F, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 263

Iteration: 1
 Score =  115 bits (288), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 61/199 (30%), Positives = 109/199 (54%), Gaps = 6/199 (3%)
Query: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
           +YD+  T++SP+GR++Q+EYAMEA+    + +G+ SK   VLV  K+  S+L   +   +
Sbjct: 5   QYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSEL---AAHQK 61
Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
           K+  +D+H+  ++AG+ +DA +L N  R +     + +  P+PV +LV  +    Q  TQ
Sbjct: 62  KILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQ 121
Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKD-- 181
             G RP+GV  L AG+D + G  ++ + PS NY   +            + L++   +  
Sbjct: 122 RYGRRPYGVGLLIAGYD-DMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM 180
Query: 182 DISREEAVQLALKVLSKTM 200
           + +  E V+  L+ L +T+
Sbjct: 181 ECNLNELVKHGLRALRETL 199

>pdb|1FNT|F Chain F, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 234

Iteration: 1
 Score =  114 bits (284), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 74/215 (34%), Positives = 107/215 (49%), Gaps = 8/215 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD  T  FSP GRL+QVEYA+EAI      +G+ S    VLV  K+   +L   S+  +K
Sbjct: 6   YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL---SSYQKK 62
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + K D+H+  ++AG+  DA +L N  R Q    +  +   + VE+    LCD  Q  TQ 
Sbjct: 63  IIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQS 122
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGN----YGGWKXXXXXXXXXXXXSILKQDYK 180
            G RP+GV  L  G+DK+ G  L    PSGN    YG                 L    K
Sbjct: 123 YGGRPYGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIK 181
Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
            D + +E ++  ++ +S+++   SLT D L +A V
Sbjct: 182 IDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIV 216

>pdb|4G4S|F Chain F, Structure Of Proteasome-Pba1-Pba2 Complex Length = 235

Iteration: 1
 Score =  114 bits (284), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 74/215 (34%), Positives = 107/215 (49%), Gaps = 8/215 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD  T  FSP GRL+QVEYA+EAI      +G+ S    VLV  K+   +L   S+  +K
Sbjct: 7   YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL---SSYQKK 63
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + K D+H+  ++AG+  DA +L N  R Q    +  +   + VE+    LCD  Q  TQ 
Sbjct: 64  IIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQS 123
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGN----YGGWKXXXXXXXXXXXXSILKQDYK 180
            G RP+GV  L  G+DK+ G  L    PSGN    YG                 L    K
Sbjct: 124 YGGRPYGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIK 182
Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
            D + +E ++  ++ +S+++   SLT D L +A V
Sbjct: 183 IDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIV 217

>pdb|1RYP|F Chain F, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 233

Iteration: 1
 Score =  114 bits (284), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 74/215 (34%), Positives = 107/215 (49%), Gaps = 8/215 (3%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD  T  FSP GRL+QVEYA+EAI      +G+ S    VLV  K+   +L   S+  +K
Sbjct: 5   YDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL---SSYQKK 61
Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + K D+H+  ++AG+  DA +L N  R Q    +  +   + VE+    LCD  Q  TQ 
Sbjct: 62  IIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQS 121
Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGN----YGGWKXXXXXXXXXXXXSILKQDYK 180
            G RP+GV  L  G+DK+ G  L    PSGN    YG                 L    K
Sbjct: 122 YGGRPYGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIK 180
Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
            D + +E ++  ++ +S+++   SLT D L +A V
Sbjct: 181 IDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIV 215

>pdb|1VSY|B Chain B, Proteasome Activator Complex Length = 231

Iteration: 1
 Score =  109 bits (273), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 64/195 (32%), Positives = 105/195 (53%), Gaps = 3/195 (1%)
Query: 20  QVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGI 79
           Q++YA+ A+    +++GI + +GVV+  EKK +S L  + T + K+  +   +    +G+
Sbjct: 1   QIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLS-KVSLLTPDIGAVYSGM 59
Query: 80  MSDANILINTAR-VQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAG 138
             D  +L++ +R V    Y   Y E  P + LV  +    Q  TQ GG+RPFGVS L AG
Sbjct: 60  GPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAG 119
Query: 139 WDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAVQLALKVLSK 198
            D+  GF LY  DPSG+Y  WK            + L++ + D++  E+A+ +AL  L +
Sbjct: 120 HDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKE 179
Query: 199 TMDSTSLTSDKLELA 213
           +++      D +ELA
Sbjct: 180 SVEG-EFNGDTIELA 193

>pdb|1G0U|G Chain G, A Gated Channel Into The Proteasome Core Particle Length = 252

Iteration: 1
 Score =  103 bits (258), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 116/241 (48%), Gaps = 13/241 (5%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAG-SAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
           YD   TIFSPEGRLYQVEYA +A      +++ +  KD  V++ +KKV  KLL   T+  
Sbjct: 12  YDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLD-PTTVS 70
Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
            ++ I   +   V G + DA      A+ +A  + Y Y   MP + L + + +  Q YTQ
Sbjct: 71  YIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQ 130
Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK--- 180
              +RP GV   F   D+  G  +Y +DP+G Y G+K            + L+  +K   
Sbjct: 131 RAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSK 190
Query: 181 -DDISREEAVQLALKVLSKTMDS--TSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            D I+ E   ++    ++  +D+  T  + + LE+       + K K+   S E + + L
Sbjct: 191 IDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVG-----VATKDKFFTLSAENIEERL 245
Query: 238 V 238
           V
Sbjct: 246 V 246

>pdb|1RYP|A Chain A, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 243

Iteration: 1
 Score =  103 bits (258), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 116/241 (48%), Gaps = 13/241 (5%)
Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAG-SAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
           YD   TIFSPEGRLYQVEYA +A      +++ +  KD  V++ +KKV  KLL   T+  
Sbjct: 3   YDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLD-PTTVS 61
Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
            ++ I   +   V G + DA      A+ +A  + Y Y   MP + L + + +  Q YTQ
Sbjct: 62  YIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQ 121
Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKXXXXXXXXXXXXSILKQDYK--- 180
              +RP GV   F   D+  G  +Y +DP+G Y G+K            + L+  +K   
Sbjct: 122 RAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSK 181
Query: 181 -DDISREEAVQLALKVLSKTMDS--TSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            D I+ E   ++    ++  +D+  T  + + LE+       + K K+   S E + + L
Sbjct: 182 IDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVG-----VATKDKFFTLSAENIEERL 236
Query: 238 V 238
           V
Sbjct: 237 V 237

>pdb|3H4P|AA Chain a, Proteasome 20s Core Particle From Methanocaldococcus Jannaschii Length = 219

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 80/184 (43%), Gaps = 5/184 (2%)
Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +G++  D V+L  +K+ +   L      +K+YKIDD++A  +AG + DA  ++     
Sbjct: 3   TTVGLICDDAVILATDKRASLGNLVADKEAKKLYKIDDYIAMTIAGSVGDAQAIVRLLIA 62
Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           +A+ Y       +P       L +       F    PF    +  G+D   G +L+  DP
Sbjct: 63  EAKLYKMRTGRNIPPLACATLLSNILHSSRMF----PFLTQIIIGGYDLLEGAKLFSLDP 118
Query: 153 SGNYGGWKXXXXXXXXXXXX-SILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLE 211
            G     K              +L+  Y  D+S EE ++LAL  L   M+  + + + + 
Sbjct: 119 LGGMNEEKTFTATGSGSPIAYGVLEAGYDRDMSVEEGIKLALNALKSAMERDTFSGNGIS 178
Query: 212 LAEV 215
           LA +
Sbjct: 179 LAVI 182

>pdb|1J2Q|H Chain H, 20s Proteasome In Complex With Calpain-inhibitor I From Archaeoglobus Fulgidus Length = 202

Iteration: 1
 Score = 66.2 bits (160), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/208 (24%), Positives = 92/208 (44%), Gaps = 11/208 (5%)
Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +G++ KDGVV+  EK+ T      S + +K+Y+I D +A   AG + DA  L    ++
Sbjct: 2   TTVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKI 61
Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           +A  Y    +    V  +     +    Y  F    P+ V  L  G D   G  +Y  DP
Sbjct: 62  EANLYEIRRERKPTVRAIATLTSNLLNSYRYF----PYLVQLLIGGIDSE-GKSIYSIDP 116
Query: 153 SGNYGGWKXXXXXXXXXXXX-SILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLE 211
            G     K              +L+  +  +I  +EAV+LA++ +   M   S + D ++
Sbjct: 117 IGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVELAVRAIYSAMKRDSASGDGID 176
Query: 212 LAEVFLMPSGKVKYQVCSPEALSKLLVK 239
           + ++      + ++   SPE + ++L K
Sbjct: 177 VVKI-----TEDEFYQYSPEEVEQILAK 199

>pdb|1YA7|H Chain H, Implications For Interactions Of Proteasome With Pan And Pa700 From The 1.9 A Structure Of A Proteasome-11s Activator Complex Length = 217

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 39/174 (22%), Positives = 78/174 (44%), Gaps = 8/174 (4%)
Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +GI  KD V++  E++VT +      + +K+++ID +    +AG++ DA +L+   + 
Sbjct: 10  TTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKA 69
Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           + + Y    +  MP+E  V +L        ++    P+ V  L  G D      ++  D 
Sbjct: 70  ELELYRLQRRVNMPIEA-VATLLSNMLNQVKY---MPYMVQLLVGGIDT--APHVFSIDA 123
Query: 153 SGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAVQLALKVLS--KTMDSTS 204
           +G                   +L+  Y + ++ +E V L ++ +S  K  DS S
Sbjct: 124 AGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQRDSAS 177

>pdb|1PMA|B Chain B, Proteasome From Thermoplasma Acidophilum Length = 211

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 39/174 (22%), Positives = 78/174 (44%), Gaps = 8/174 (4%)
Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +GI  KD V++  E++VT +      + +K+++ID +    +AG++ DA +L+   + 
Sbjct: 10  TTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKA 69
Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           + + Y    +  MP+E  V +L        ++    P+ V  L  G D      ++  D 
Sbjct: 70  ELELYRLQRRVNMPIEA-VATLLSNMLNQVKY---MPYMVQLLVGGIDT--APHVFSIDA 123
Query: 153 SGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAVQLALKVLS--KTMDSTS 204
           +G                   +L+  Y + ++ +E V L ++ +S  K  DS S
Sbjct: 124 AGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQRDSAS 177

>pdb|3C91|H Chain H, Thermoplasma Acidophilum 20s Proteasome With An Open Gate Length = 203

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 39/174 (22%), Positives = 78/174 (44%), Gaps = 8/174 (4%)
Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +GI  KD V++  E++VT +      + +K+++ID +    +AG++ DA +L+   + 
Sbjct: 2   TTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKA 61
Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           + + Y    +  MP+E  V +L        ++    P+ V  L  G D      ++  D 
Sbjct: 62  ELELYRLQRRVNMPIEA-VATLLSNMLNQVKY---MPYMVQLLVGGIDT--APHVFSIDA 115
Query: 153 SGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAVQLALKVLS--KTMDSTS 204
           +G                   +L+  Y + ++ +E V L ++ +S  K  DS S
Sbjct: 116 AGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQRDSAS 169

>pdb|3UNF|H Chain H, Mouse 20s Immunoproteasome In Complex With Pr-957 Length = 234

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 36/165 (21%), Positives = 75/165 (45%), Gaps = 12/165 (7%)
Query: 36  GILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQ 95
           G++ +DGV+L  + + T+  +    S EK++ I   + C  AG+ +D  +    A  + +
Sbjct: 5   GLVFRDGVILGADTRATNDSVVADKSCEKIHFIAPKIYCCGAGVAADTEMTTRMAASKME 64
Query: 96  RYTYAY-QEP--MPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
            +  +  +EP    V ++++      QG+         G S +  G D N G QLY   P
Sbjct: 65  LHALSTGREPRVATVTRILRQTLFRYQGH--------VGASLVVGGVDLN-GPQLYEVHP 115
Query: 153 SGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAVQLALKVLS 197
            G+Y                ++L+  ++ +++ E A +L ++ ++
Sbjct: 116 HGSYSRLPFTALGSGQGAAVALLEDRFQPNMTLEAAQELLVEAIT 160

>pdb|1IRU|K Chain K, Crystal Structure Of The Mammalian 20s Proteasome At 2.75 A Resolution Length = 201

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 41/168 (24%), Positives = 66/168 (39%), Gaps = 10/168 (5%)
Query: 35  IGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD----ANILINTA 90
           IGI   D V++  ++   S ++Q     +KM+K+ + +     G   D    A  +    
Sbjct: 5   IGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNV 64
Query: 91  RVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMS 150
           ++   R  Y            ++L D  +  T      P+ V+ L AG+D++ G  LY  
Sbjct: 65  QLYKMRNGYELSPTAAANFTRRNLADCLRSRT------PYHVNLLLAGYDEHEGPALYYM 118
Query: 151 DPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAVQLALKVLSK 198
           D                     SIL + Y   ISRE AV+L  K L +
Sbjct: 119 DYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEE 166

>pdb|3UNB|J Chain J, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 201

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 41/168 (24%), Positives = 66/168 (39%), Gaps = 10/168 (5%)
Query: 35  IGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD----ANILINTA 90
           IGI   D V++  ++   S ++Q     +KM+K+ + +     G   D    A  +    
Sbjct: 5   IGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNV 64
Query: 91  RVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMS 150
           ++   R  Y            ++L D  +  T      P+ V+ L AG+D++ G  LY  
Sbjct: 65  QLYKMRNGYELSPTAAANFTRRNLADCLRSRT------PYHVNLLLAGYDEHEGPALYYM 118
Query: 151 DPSGNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAVQLALKVLSK 198
           D                     SIL + Y   ISRE AV+L  K L +
Sbjct: 119 DYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEE 166

>pdb|1G0U|L Chain L, A Gated Channel Into The Proteasome Core Particle Length = 241

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 31/147 (21%), Positives = 64/147 (43%), Gaps = 6/147 (4%)
Query: 12  FSPEGRLYQVEYAMEAIG-NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDD 70
           +S E     +E+     G N G+ +GI  +D  VL G+ +  +     S    K++   D
Sbjct: 8   YSSEASNTPIEHQFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGD 67
Query: 71  HVACAVAGIMSDANILINTARVQAQRYTYAYQE-PMPVEQLVQSLCDTKQGYTQFGGLRP 129
           ++  +  G  +D + L+   +   + Y + + +  + +    +++     G   F    P
Sbjct: 68  NIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKRFF----P 123
Query: 130 FGVSFLFAGWDKNYGFQLYMSDPSGNY 156
           + V  + AG D++    +Y  DP G+Y
Sbjct: 124 YYVHTIIAGLDEDGKGAVYSFDPVGSY 150

>pdb|3UNB|N Chain N, Mouse Constitutive 20s Proteasome In Complex With Pr-957 Length = 205

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 35/177 (19%), Positives = 66/177 (37%), Gaps = 11/177 (6%)
Query: 42  GVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAY 101
           GVVL  + + T+     +  T+K+  I DH+ C  +G  +D   + +    Q   ++   
Sbjct: 11  GVVLGADSRTTTGSYIANRVTDKLTPIHDHIFCCRSGSAADTQAVADAVTYQLGFHSIEL 70
Query: 102 QEPMPVE---QLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGG 158
            EP  V     L + +C   +     G         + AGWD   G Q+Y     G    
Sbjct: 71  NEPPLVHTAASLFKEMCYRYREDLMAG--------IIIAGWDPQEGGQVYSVPMGGMMVR 122
Query: 159 WKXXXXXXXXXXXXSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
                           +   Y++ ++++E +Q     L+  M+    +   + LA +
Sbjct: 123 QSFAIGGSGSSYIYGYVDATYREGMTKDECLQFTANALALAMERDGSSGGVIRLAAI 179

>pdb|1RYP|I Chain I, Crystal Structure Of The 20s Proteasome From Yeast At 2.4 Angstroms Resolution Length = 222

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 35/159 (22%), Positives = 70/159 (44%), Gaps = 8/159 (5%)
Query: 35  IGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQA 94
           +G+   +GVV+  + + T   +    +  K+++I   + CA AG  +D   +        
Sbjct: 4   VGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNI 63
Query: 95  QRYT-YAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPS 153
           + ++ Y  +EP    ++V +L   KQ   ++ G    G   + AG D   G  L+     
Sbjct: 64  ELHSLYTSREP----RVVSALQMLKQHLFKYQG--HIGAYLIVAGVDPT-GSHLFSIHAH 116
Query: 154 GNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAVQLA 192
           G+                 ++L+  +K D+++EEA++LA
Sbjct: 117 GSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLA 155

>pdb|1FNT|I Chain I, Crystal Structure Of The 20s Proteasome From Yeast In Complex With The Proteasome Activator Pa26 From Trypanosome Brucei At 3.2 Angstroms Resolution Length = 232

Iteration: 1
 Score = 40.4 bits (93), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 35/159 (22%), Positives = 70/159 (44%), Gaps = 8/159 (5%)
Query: 35  IGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQA 94
           +G+   +GVV+  + + T   +    +  K+++I   + CA AG  +D   +        
Sbjct: 4   VGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNI 63
Query: 95  QRYT-YAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPS 153
           + ++ Y  +EP    ++V +L   KQ   ++ G    G   + AG D   G  L+     
Sbjct: 64  ELHSLYTSREP----RVVSALQMLKQHLFKYQG--HIGAYLIVAGVDPT-GSHLFSIHAH 116
Query: 154 GNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAVQLA 192
           G+                 ++L+  +K D+++EEA++LA
Sbjct: 117 GSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLA 155

>pdb|3NZJ|H Chain H, Crystal Structure Of Yeast 20s Proteasome In Complex With Ligand 2a Length = 261

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 35/159 (22%), Positives = 70/159 (44%), Gaps = 8/159 (5%)
Query: 35  IGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQA 94
           +G+   +GVV+  + + T   +    +  K+++I   + CA AG  +D   +        
Sbjct: 33  VGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNI 92
Query: 95  QRYT-YAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPS 153
           + ++ Y  +EP    ++V +L   KQ   ++ G    G   + AG D   G  L+     
Sbjct: 93  ELHSLYTSREP----RVVSALQMLKQHLFKYQG--HIGAYLIVAGVDPT-GSHLFSIHAH 145
Query: 154 GNYGGWKXXXXXXXXXXXXSILKQDYKDDISREEAVQLA 192
           G+                 ++L+  +K D+++EEA++LA
Sbjct: 146 GSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLA 184

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	250
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	1e-124
1iru_C	261	20S proteasome; cell cycle, immune response, prote	1e-120
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	1e-119
1iru_B	233	20S proteasome; cell cycle, immune response, prote	1e-118
1iru_E	241	20S proteasome; cell cycle, immune response, prote	1e-117
1iru_A	246	20S proteasome; cell cycle, immune response, prote	1e-116
1iru_G	254	20S proteasome; cell cycle, immune response, prote	1e-116
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	1e-115
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	1e-114
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	1e-113
1iru_F	263	20S proteasome; cell cycle, immune response, prote	1e-113
1iru_D	248	20S proteasome; cell cycle, immune response, prote	1e-113
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	1e-112
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	1e-112
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	1e-111
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	1e-111
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	1e-110
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	1e-109
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	4e-68
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	6e-64
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	1e-63
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	8e-50
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	2e-49
1iru_I	234	20S proteasome; cell cycle, immune response, prote	4e-49
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	2e-44
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	1e-42
1q5r_H	294	Proteasome beta-type subunit 1; proteasome assembl	5e-36
3nzj_K	287	Proteasome component PRE2; ubiquitin, protein degr	2e-34
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	3e-33
1iru_L	204	20S proteasome; cell cycle, immune response, prote	1e-32
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	5e-32
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	5e-31
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	2e-30
1ryp_H	205	20S proteasome; multicatalytic proteinase, protein	6e-28
1iru_H	205	20S proteasome; cell cycle, immune response, prote	2e-27
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	2e-26
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	2e-26
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	1e-25
1iru_K	201	20S proteasome; cell cycle, immune response, prote	4e-25
1iru_J	205	20S proteasome; cell cycle, immune response, prote	5e-25
1iru_M	213	20S proteasome; cell cycle, immune response, prote	1e-24
1ryp_J	204	20S proteasome; multicatalytic proteinase, protein	6e-24
1g0u_M	266	Proteasome component PRE4; ubiquitin, degradation,	2e-21
1ryp_N	233	20S proteasome; multicatalytic proteinase, protein	3e-21
1iru_N	219	20S proteasome; cell cycle, immune response, prote	5e-19
1g3k_A	174	ATP-dependent protease HSLV; hydrolase; 1.90A {Hae	2e-06

>1ryp_C 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_B* 1g65_B 2f16_B* 2fak_B* 2fny_B* 2gpl_B* 3d29_B* 3dy3_B* 3dy4_B* 3e47_B* 3gpj_B* 3gpt_B* 3gpw_B* 3hye_B* 3mg0_B* 3mg4_B* 3okj_B* 3shj_B* 3tdd_B* 3nzj_B* ... Length = 244

 Score =  352 bits (906), Expect = e-124
 Identities = 147/243 (60%), Positives = 191/243 (78%), Gaps = 1/243 (0%)

Query: 2   SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
           SRRYDSRTTIFSPEGRLYQVEYA+E+I +AG+AIGI++ DG+VL  E+KVTS LL+  TS
Sbjct: 2   SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 61

Query: 62  TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
           TEK+YK++D +A AVAG+ +DA ILINTAR+ AQ Y   Y E +PVE LV+ L D KQGY
Sbjct: 62  TEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGY 121

Query: 122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD 181
           TQ GGLRPFGVSF++AG+D  YG+QLY S+PSGNY GWKA ++GAN  AAQ++L+ DYKD
Sbjct: 122 TQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 181

Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEV-FLMPSGKVKYQVCSPEALSKLLVKH 240
           D+  ++A++LALK LSKT DS++LT D+LE A +      G+V  ++  P+ +  +LVK 
Sbjct: 182 DMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKT 241

Query: 241 GVT 243
           G+T
Sbjct: 242 GIT 244

>1iru_C 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_B* 3une_B 3unf_B* 3unh_B Length = 261

 Score =  342 bits (880), Expect = e-120
 Identities = 146/249 (58%), Positives = 190/249 (76%), Gaps = 2/249 (0%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           MSRRYDSRTTIFSPEGRLYQVEYAMEAIG+AG+ +GIL+ DGV+L  E++   KLL    
Sbjct: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
            +EK+YK+++ +AC+VAGI SDAN+L N  R+ AQRY   YQEP+P EQLV +LCD KQ 
Sbjct: 61  FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA 120

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQFGG RPFGVS L+ GWDK+YGFQLY SDPSGNYGGWKA  IG N+ AA S+LKQDYK
Sbjct: 121 YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK 180

Query: 181 D-DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
           + +++ + A+ LA+KVL+KTMD + L+++K+E+A +    +GK   +V   + + +L+ K
Sbjct: 181 EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATL-TRENGKTVIRVLKQKEVEQLIKK 239

Query: 240 HGVTQPAAE 248
           H   +  AE
Sbjct: 240 HEEEEAKAE 248

>1ryp_B 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_B 1g0u_A* 1jd2_A* 1g65_A 1z7q_B 2f16_A* 2fak_A* 2fny_A* 2gpl_A* 2zcy_A* 3bdm_A* 3d29_A* 3dy3_A* 3dy4_A* 3e47_A* 3gpj_A* 3gpt_A* 3gpw_A* 3hye_A* 3mg0_A* ... Length = 250

 Score =  339 bits (873), Expect = e-119
 Identities = 80/251 (31%), Positives = 133/251 (52%), Gaps = 14/251 (5%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           M+ RY    T FSP G+L Q++YA+ A+    +++GI + +GVV+  EKK +S L  + T
Sbjct: 1   MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET 60

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQ-RYTYAYQEPMPVEQLVQSLCDTKQ 119
              K+  +   +    +G+  D  +L++ +R  A   Y   Y E  P + LV  +    Q
Sbjct: 61  L-SKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQ 119

Query: 120 GYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDY 179
             TQ GG+RPFGVS L AG D+  GF LY  DPSG+Y  WKA AIG  + AA++ L++ +
Sbjct: 120 EATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRW 179

Query: 180 KDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV-----------FLMPSGKVKYQVC 228
            D++  E+A+ +AL  L ++++      D +ELA +            +      +++  
Sbjct: 180 NDELELEDAIHIALLTLKESVE-GEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKL 238

Query: 229 SPEALSKLLVK 239
           + + ++  L  
Sbjct: 239 TSQEINDRLEA 249

>1iru_B 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_A* 3une_A 3unf_A* 3unh_A Length = 233

 Score =  336 bits (864), Expect = e-118
 Identities = 85/238 (35%), Positives = 128/238 (53%), Gaps = 8/238 (3%)

Query: 2   SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
            R Y    T FSP G+L Q+EYA+ A+     ++GI + +GVVL  EKK  S L     S
Sbjct: 2   ERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER-S 60

Query: 62  TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
             K+  I  H+    +G+  D  +L++ AR  AQ+Y   YQEP+P  QLVQ +    Q Y
Sbjct: 61  VHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEY 120

Query: 122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD 181
           TQ GG+RPFGVS L  GW++     L+ SDPSG Y  WKA A+G N    ++ L++ Y +
Sbjct: 121 TQSGGVRPFGVSLLICGWNEG-RPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE 179

Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
           D+  E+A+  A+  L ++ +   +T D +E+         +  ++  +P  +   L  
Sbjct: 180 DLELEDAIHTAILTLKESFE-GQMTEDNIEVGIC-----NEAGFRRLTPTEVKDYLAA 231

>1iru_E 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_D* 3une_D 3unf_D* 3unh_D Length = 241

 Score =  333 bits (856), Expect = e-117
 Identities = 90/245 (36%), Positives = 145/245 (59%), Gaps = 13/245 (5%)

Query: 1   MSR-RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTS 59
           ++R  YD     FSPEGRL+QVEY +EAI    +AIGI + +GV L  EK++TS L++ S
Sbjct: 3   LTRSEYDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPS 62

Query: 60  TSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQ 119
            S EK+ +ID H+ CA++G+++DA  LI+ ARV+ Q + + Y E M VE + Q++ +   
Sbjct: 63  -SIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLAL 121

Query: 120 GYTQFGGL-----RPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSI 174
            + +         RPFGV+ LF G D+  G QL+  DPSG +    A AIG+ ++ AQS 
Sbjct: 122 QFGEEDADPGAMSRPFGVALLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSASEGAQSS 180

Query: 175 LKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALS 234
           L++ Y   ++ +EA++ +L +L + M+   L +  +ELA V         + + + E L 
Sbjct: 181 LQELYHKSMTLKEAIKSSLIILKQVME-EKLNATNIELATV----QPGQNFHMFTKEELE 235

Query: 235 KLLVK 239
           +++  
Sbjct: 236 EVIKD 240

>1iru_A 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_G* 3une_G 3unf_G* 3unh_G Length = 246

 Score =  332 bits (854), Expect = e-116
 Identities = 81/246 (32%), Positives = 130/246 (52%), Gaps = 12/246 (4%)

Query: 1   MSR----RYDSRTTIFSPEGRLYQVEYAMEAIGNAGS-AIGILSKDGVVLVGEKKVTSKL 55
           MSR     +D   TIFSPEGRLYQVEYA +AI   G  ++ +  KD  V+V +KKV  KL
Sbjct: 1   MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL 60

Query: 56  LQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLC 115
           L +S +   ++KI +++ C + G+ +D+   +  AR +A  + Y Y   +PV+ L + + 
Sbjct: 61  LDSS-TVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIA 119

Query: 116 DTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSIL 175
           D  Q YTQ   +RP G   +  G D+  G Q+Y  DP+G Y G+KA A G     + S L
Sbjct: 120 DISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFL 179

Query: 176 KQDYKD--DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEAL 233
           ++  K   D + E+ V+ A+  LS  +        ++E+    ++     K+++ +   +
Sbjct: 180 EKKVKKKFDWTFEQTVETAITCLSTVLS-IDFKPSEIEVG---VVTVENPKFRILTEAEI 235

Query: 234 SKLLVK 239
              LV 
Sbjct: 236 DAHLVA 241

>1iru_G 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_F* 3une_F 3unf_F* 3unh_F Length = 254

 Score =  332 bits (852), Expect = e-116
 Identities = 82/248 (33%), Positives = 136/248 (54%), Gaps = 4/248 (1%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           +   YD   + FSP+GR++QVEYAM+A+ N+ +AIGI  KDGVV   EK V SKL +   
Sbjct: 3   IGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEG- 61

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           S ++++ +D HV  AVAG+++DA  L + AR +A  +   +   +P++ L   +      
Sbjct: 62  SNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHA 121

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YT +  +RPFG SF+   +  N G QLYM DPSG   G+   AIG   QAA++ +++   
Sbjct: 122 YTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQM 181

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
            +++  + V+   K++    D     + +LEL+ V  + +G+ +     P+ + +   K+
Sbjct: 182 KEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEI---VPKDIREEAEKY 238

Query: 241 GVTQPAAE 248
                  E
Sbjct: 239 AKESLKEE 246

>1ryp_A 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_G* 1g65_G 1vsy_A 2f16_G* 2fak_G* 2fny_G* 2gpl_G* 3d29_G* 3dy3_G* 3dy4_G* 3e47_G* 3gpj_G* 3gpt_G* 3gpw_G* 3hye_G* 3l5q_A 3mg0_G* 3mg4_G* 3oeu_G* 3oev_G* ... Length = 243

 Score =  329 bits (847), Expect = e-115
 Identities = 76/244 (31%), Positives = 118/244 (48%), Gaps = 15/244 (6%)

Query: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGNAGS-AIGILSKDGVVLVGEKKVTSKLLQTSTST 62
            YD   TIFSPEGRLYQVEYA +A       ++ +  KD  V++ +KKV  KLL  + + 
Sbjct: 2   GYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPT-TV 60

Query: 63  EKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYT 122
             ++ I   +   V G + DA      A+ +A  + Y Y   MP + L + + +  Q YT
Sbjct: 61  SYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYT 120

Query: 123 QFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK-- 180
           Q   +RP GV   F   D+  G  +Y +DP+G Y G+KA A G   Q   + L+  +K  
Sbjct: 121 QRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKS 180

Query: 181 -----DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSK 235
                ++ S E+ V+ A+  +   +  T  + + LE+         K K+   S E + +
Sbjct: 181 KIDHINEESWEKVVEFAITHMIDALG-TEFSKNDLEVGVA-----TKDKFFTLSAENIEE 234

Query: 236 LLVK 239
            LV 
Sbjct: 235 RLVA 238

>3nzj_F Proteasome component C1; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 1z7q_G* 3nzw_F* 3nzx_F* 3un4_F* 3un8_F* 3bdm_F* 1fnt_G* 2zcy_F* Length = 288

 Score =  328 bits (844), Expect = e-114
 Identities = 81/240 (33%), Positives = 132/240 (55%), Gaps = 6/240 (2%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           +   YD   ++FSP+GR +QVEYA++A+ N  ++IGI   DGVV   EK +TSKLL    
Sbjct: 4   IGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQ- 62

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
              K+  +D H+ C  +G++ D   L+N  R +A  +   Y+ P+P+      L    Q 
Sbjct: 63  KNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQA 122

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQ--- 177
           +T +  +RPFGVS +F G DKN G  LYM +PSG+Y G+K AA G   Q+A++ L++   
Sbjct: 123 HTLYNSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVD 181

Query: 178 DYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            + + +S  EAV+ A K++    +       +LE++   L  +    ++    + L + +
Sbjct: 182 HHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNG-LHKFVKGDLLQEAI 240

>1ryp_G 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_F* 1g65_F 1vsy_G 2f16_F* 2fak_F* 2fny_F* 2gpl_F* 3d29_F* 3dy3_F* 3dy4_F* 3e47_F* 3gpj_F* 3gpt_F* 3gpw_F* 3hye_F* 3l5q_L 3mg0_F* 3mg4_F* 3okj_F* 3shj_F* ... Length = 244

 Score =  325 bits (835), Expect = e-113
 Identities = 81/237 (34%), Positives = 131/237 (55%), Gaps = 6/237 (2%)

Query: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
            YD   ++FSP+GR +QVEYA++A+ N  ++IGI   DGVV   EK +TSKLL       
Sbjct: 3   GYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQ-KNV 61

Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
           K+  +D H+ C  +G++ D   L+N  R +A  +   Y+ P+P+      L    Q +T 
Sbjct: 62  KIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTL 121

Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQ---DYK 180
           +  +RPFGVS +F G DKN G  LYM +PSG+Y G+K AA G   Q+A++ L++    + 
Sbjct: 122 YNSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHP 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
           + +S  EAV+ A K++    +       +LE++   L  +    ++    + L + +
Sbjct: 181 EGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNG-LHKFVKGDLLQEAI 236

>1iru_F 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_E* 3une_E 3unf_E* 3unh_E Length = 263

 Score =  324 bits (834), Expect = e-113
 Identities = 74/243 (30%), Positives = 133/243 (54%), Gaps = 12/243 (4%)

Query: 1   MSR-RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTS 59
           M R +YD+  T++SP+GR++Q+EYAMEA+    + +G+ SK   VLV  K+  S+L    
Sbjct: 1   MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ 60

Query: 60  TSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQ 119
               K+  +D+H+  ++AG+ +DA +L N  R +     + +  P+PV +LV  +    Q
Sbjct: 61  K---KILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQ 117

Query: 120 GYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDY 179
             TQ  G RP+GV  L AG+D   G  ++ + PS NY   +A +IGA +Q+A++ L++  
Sbjct: 118 IPTQRYGRRPYGVGLLIAGYDDM-GPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHM 176

Query: 180 KD--DISREEAVQLALKVLSKTMDST-SLTSDKLELAEVFLMPSGKVKYQVCSPEALSKL 236
            +  + +  E V+  L+ L +T+ +   LT+  + +  V       +++ +   + +S  
Sbjct: 177 SEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIV----GKDLEFTIYDDDDVSPF 232

Query: 237 LVK 239
           L  
Sbjct: 233 LEG 235

>1iru_D 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unf_C* 3une_C* 3unh_C 3unb_C* Length = 248

 Score =  323 bits (830), Expect = e-113
 Identities = 85/237 (35%), Positives = 135/237 (56%), Gaps = 10/237 (4%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+G L+QVEYA EA+    +A+G+  +D VVL  EKK  +KL    T   K
Sbjct: 3   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTV-RK 61

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +DD+V  A AG+ +DA I+IN ARV+ Q +    ++P+ VE + + +   KQ YTQ 
Sbjct: 62  ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQS 121

Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDD-- 182
            G RPFG+S L  G+D +   +LY +DPSG Y  WKA AIG   ++ +  L+++Y D+  
Sbjct: 122 NGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAI 181

Query: 183 ISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
            + +  ++L +K L + +         +ELA +          ++ +PE + K + +
Sbjct: 182 ETDDLTIKLVIKALLEVVQ---SGGKNIELAVM----RRDQSLKILNPEEIEKYVAE 231

>1yar_A Proteasome alpha subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase-HYD activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_A 1pma_A 3c91_A 3c92_A 3ipm_A 2ku1_A 2ku2_A 1yau_A 3jrm_A 3jse_A 3jtl_A Length = 233

 Score =  322 bits (827), Expect = e-112
 Identities = 90/240 (37%), Positives = 148/240 (61%), Gaps = 10/240 (4%)

Query: 1   MSR---RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQ 57
           M +    Y    T+FSP+GRL+QVEYA EA+    +A+G+   +GV+L+ +KKV S+L++
Sbjct: 1   MQQGQMAYSRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIE 60

Query: 58  TSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDT 117
            + S EK+  IDD+VA   +G+++DA +L++ AR+ AQ+    Y   + +E LV+ + D 
Sbjct: 61  QN-SIEKIQLIDDYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQ 119

Query: 118 KQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQ 177
            Q YTQ+GG+RP+GVS +FAG D+  G +L+  DP+G    +KA AIG+   A  S L++
Sbjct: 120 MQQYTQYGGVRPYGVSLIFAGIDQI-GPRLFDCDPAGTINEYKATAIGSGKDAVVSFLER 178

Query: 178 DYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
           +YK+++  +EAV L +K L  +++         E+A +    +   KY++   E + K L
Sbjct: 179 EYKENLPEKEAVTLGIKALKSSLE-EGEELKAPEIASI----TVGNKYRIYDQEEVKKFL 233

>1ryp_F 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_E* 1g65_E 2f16_E* 2fak_E* 2fny_E* 2gpl_E* 3d29_E* 3dy3_E* 3dy4_E* 3e47_E* 3gpj_E* 3gpt_E* 3gpw_E* 3hye_E* 3mg0_E* 3mg4_E* 3oeu_E* 3oev_E* 3okj_E* 3shj_E* ... Length = 233

 Score =  321 bits (824), Expect = e-112
 Identities = 80/238 (33%), Positives = 123/238 (51%), Gaps = 12/238 (5%)

Query: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
            YD  T  FSP GRL+QVEYA+EAI      +G+ S    VLV  K+   +L   S+  +
Sbjct: 4   NYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL---SSYQK 60

Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
           K+ K D+H+  ++AG+  DA +L N  R Q    +  +   + VE+    LCD  Q  TQ
Sbjct: 61  KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQ 120

Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD-- 181
             G RP+GV  L  G+DK+ G  L    PSGN       AIGA +Q A++ L++      
Sbjct: 121 SYGGRPYGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI 179

Query: 182 --DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
             D + +E ++  ++ +S+++   SLT D L +A V         + +   EA++K +
Sbjct: 180 KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIV----GKDTPFTIYDGEAVAKYI 233

>1ryp_E 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_D* 1g65_D 2f16_D* 2fak_D* 2fny_D* 2gpl_D* 3d29_D* 3dy3_D* 3dy4_D* 3e47_D* 3gpj_D* 3gpt_D* 3gpw_D* 3hye_D* 3mg0_D* 3mg4_D* 3okj_D* 3shj_D* 3tdd_D* 2z5c_C ... Length = 242

 Score =  318 bits (816), Expect = e-111
 Identities = 87/240 (36%), Positives = 143/240 (59%), Gaps = 12/240 (5%)

Query: 6   DSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKM 65
           D   + FSPEGRL+QVEY++EAI    +AIGI +K+GVVL  EK+ TS LL++  S EK+
Sbjct: 1   DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESD-SIEKI 59

Query: 66  YKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFG 125
            +ID H+ CA++G+ +DA  +I  AR  A  +   Y E + VE L QS+CD    + +  
Sbjct: 60  VEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGA 119

Query: 126 ------GLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDY 179
                   RPFGV+ L AG D + G+QL+ ++PSG +  + A AIG+ ++ AQ+ L  ++
Sbjct: 120 SGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEW 179

Query: 180 KDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
              ++ +EA  L LK+L + M+   L  +  +L+ +    + +  +++   E  ++L+ +
Sbjct: 180 HSSLTLKEAELLVLKILKQVME-EKLDENNAQLSCI----TKQDGFKIYDNEKTAELIKE 234

>3h4p_A Proteasome subunit alpha; core particle, cytoplasm, hydrolase, protease, threonine protease; 4.10A {Methanocaldococcus jannaschii} Length = 264

 Score =  318 bits (817), Expect = e-111
 Identities = 101/249 (40%), Positives = 155/249 (62%), Gaps = 7/249 (2%)

Query: 2   SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
              YD   T+FSPEGRLYQVEYA EA+    +AIGI  KDGVVL  ++++TSKL++   S
Sbjct: 9   PSAYDRAITVFSPEGRLYQVEYAREAVRRGTTAIGIACKDGVVLAVDRRITSKLVKIR-S 67

Query: 62  TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
            EK+++IDDHVA A +G+++DA +LI+ AR++AQ Y   Y E + +E L + +CD KQ Y
Sbjct: 68  IEKIFQIDDHVAAATSGLVADARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAY 127

Query: 122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD 181
           TQ GG+RPFGVS L AG DKN   +L+ +DPSG    +KA AIG+       +L+++Y+D
Sbjct: 128 TQHGGVRPFGVSLLIAGIDKN-EARLFETDPSGALIEYKATAIGSGRPVVMELLEKEYRD 186

Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHG 241
           DI+ +E ++LA+  L+K  +   +  + +++    ++     +++    E + KL+ K  
Sbjct: 187 DITLDEGLELAITALTKANE--DIKPENVDVC---IITVKDAQFKKIPVEEIKKLIEKVK 241

Query: 242 VTQPAAETS 250
                    
Sbjct: 242 KKLNEENKK 250

>1ryp_D 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_C* 1g65_C 2f16_C* 2fak_C* 2fny_C* 2gpl_C* 3d29_C* 3dy3_C* 3dy4_C* 3e47_C* 3gpj_C* 3gpt_C* 3gpw_C* 3hye_C* 3mg0_C* 3mg4_C* 3oeu_C* 3oev_C* 3okj_C* 3shj_C* ... Length = 241

 Score =  317 bits (814), Expect = e-110
 Identities = 83/239 (34%), Positives = 135/239 (56%), Gaps = 11/239 (4%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   +IFSP+G ++QVEYA+EA+     A+G+  K+ VVL  E++ T KL  T  +  K
Sbjct: 2   YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 61

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + KID HV  + +G+ +D+ ILI  ARV+AQ +    ++P+ VE L + +   +Q YTQ 
Sbjct: 62  VSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQS 121

Query: 125 GGLRPFGVSFLFAGWDK-NYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK--- 180
           GG+RPFGVS L AG+D  +   +LY ++PSG Y  W A  IG N++  +  L+++Y    
Sbjct: 122 GGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKE 181

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
              + EE V+L ++ L + +      +  +E+  V             S E +++ + +
Sbjct: 182 PPATVEECVKLTVRSLLEVVQ---TGAKNIEITVV----KPDSDIVALSSEEINQYVTQ 233

>1j2p_A Alpha-ring, proteasome alpha subunit; hydrolase; 2.60A {Archaeoglobus fulgidus} SCOP: d.153.1.4 PDB: 1j2q_A* Length = 246

 Score =  313 bits (803), Expect = e-109
 Identities = 94/240 (39%), Positives = 152/240 (63%), Gaps = 8/240 (3%)

Query: 1   MSRR-YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTS 59
           + +  YD   T+FSP+GRL+QVEYA EA+    +AIGI  K+GV+L+ +K+V SKLL+  
Sbjct: 3   LPQMGYDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEKD 62

Query: 60  TSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQ 119
            + EK+YKID+H+  A +G+++DA +LI+ AR++AQ     Y  P+ V++L + +CD KQ
Sbjct: 63  -TIEKIYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQ 121

Query: 120 GYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDY 179
            YTQ+GG+RPFGVS L AG ++    +LY +DPSG    +KA AIG    A     +++Y
Sbjct: 122 QYTQYGGVRPFGVSLLIAGVNE--VPKLYETDPSGALLEYKATAIGMGRMAVTEFFEKEY 179

Query: 180 KDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
           +DD+S ++A+ L L  +  +++ + L  + +E+     +      ++  SPE L   + +
Sbjct: 180 RDDLSFDDAMVLGLVAMGLSIE-SELVPENIEVG---YVKVDDRTFKEVSPEELKPYVER 235

>3mi0_A Proteasome subunit alpha; enzyme inhibitors, lactones, proteasome endopeptidase comple mycobacterium tuberculosis, hydrolase; HET: SA6; 2.20A {Mycobacterium tuberculosis} PDB: 3h6f_A 3krd_A* 3h6i_A* 3mka_A 2fhh_A* 2fhg_A 3hfa_D 3hf9_A 3mfe_D Length = 248

 Score =  209 bits (533), Expect = 4e-68
 Identities = 57/250 (22%), Positives = 94/250 (37%), Gaps = 22/250 (8%)

Query: 13  SPEGRLYQ-VEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDH 71
           SPE  + +  E A + I  A S + +    GV+ V E          S S +K+ ++ D 
Sbjct: 8   SPEQAMRERSELARKGIARAKSVVALAYAGGVLFVAENP--------SRSLQKISELYDR 59

Query: 72  VACAVAGIMSDANILINTARVQAQRYTYAY-QEPMPVEQLVQSLCDTKQGYTQFGGLRPF 130
           V  A AG  ++ + L       A    YAY +  +   QL      T          +P+
Sbjct: 60  VGFAAAGKFNEFDNLRRGGIQFADTRGYAYDRRDVTGRQLANVYAQTLGT-IFTEQAKPY 118

Query: 131 GVSFLFAGWD---KNYGFQLYMSDPSGNYG-GWKAAAIGANNQAAQSILKQDYKDDISRE 186
            V    A      +    +LY     G+         +G   +   + LK+ Y ++ S  
Sbjct: 119 EVELCVAEVAHYGETKRPELYRITYDGSIADEPHFVVMGGTTEPIANALKESYAENASLT 178

Query: 187 EAVQLALKVLSKTMDSTS------LTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
           +A+++A+  L      TS      L    LE+A V      +  ++  +  AL  LLV  
Sbjct: 179 DALRIAVAALRAGSADTSGGDQPTLGVASLEVA-VLDANRPRRAFRRITGSALQALLVDQ 237

Query: 241 GVTQPAAETS 250
              Q   E+S
Sbjct: 238 ESPQSDGESS 247

>1q5q_A Proteasome alpha-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, RH erythropolis, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4 PDB: 2h6j_A 1q5r_A Length = 259

 Score =  199 bits (507), Expect = 6e-64
 Identities = 47/249 (18%), Positives = 90/249 (36%), Gaps = 22/249 (8%)

Query: 13  SPEGRLYQ-VEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDH 71
           S E  +    E A + I    S + +  +DGV+ V E          ST+  K+ ++ D 
Sbjct: 8   SAEQIMRDRSELARKGIARGRSVVVLTFRDGVLFVAENP--------STALHKVSELYDR 59

Query: 72  VACAVAGIMSDANILINTARVQAQRYTYAY-QEPMPVEQLVQSLCDT-KQGYTQFGGLRP 129
           +  A  G  ++   L     V A    Y+Y +  +    L  +   T    +T+    +P
Sbjct: 60  LGFAAVGKYNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFTE--QPKP 117

Query: 130 FGVSFLFA---GWDKNYGFQLYMSDPSGNYGGWK-AAAIGANNQAAQSILKQDYKDDISR 185
           + V    A           QLY     G+    +    +G   +   + +++ Y+ D+  
Sbjct: 118 YEVEICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADLDL 177

Query: 186 EEAVQLALKVLSKTMDSTS----LTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHG 241
           E AV +A+  L +          +    LE+A V      +  ++  +  AL +L+    
Sbjct: 178 EAAVGIAVNALRQGGAGEGEKRNVDVASLEVA-VLDQSRPRRAFRRIAGTALEQLVPAEP 236

Query: 242 VTQPAAETS 250
                +   
Sbjct: 237 AAASESAPE 245

>3unf_H Proteasome subunit beta type-10; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_H Length = 234

 Score =  197 bits (503), Expect = 1e-63
 Identities = 40/183 (21%), Positives = 83/183 (45%), Gaps = 6/183 (3%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           +  G++ +DGV+L  + + T+  +    S EK++ I   + C  AG+ +D  +    A  
Sbjct: 2   TIAGLVFRDGVILGADTRATNDSVVADKSCEKIHFIAPKIYCCGAGVAADTEMTTRMAAS 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           + + +  +      V  + + L  T   Y         G S +  G D N G QLY   P
Sbjct: 62  KMELHALSTGREPRVATVTRILRQTLFRYQG-----HVGASLVVGGVDLN-GPQLYEVHP 115

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLEL 212
            G+Y      A+G+   AA ++L+  ++ +++ E A +L ++ ++  + S   +   ++ 
Sbjct: 116 HGSYSRLPFTALGSGQGAAVALLEDRFQPNMTLEAAQELLVEAITAGILSDLGSGGNVDA 175

Query: 213 AEV 215
             +
Sbjct: 176 CVI 178

>3nzj_H Proteasome component PUP1; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_H* 3nzx_H* Length = 261

 Score =  163 bits (414), Expect = 8e-50
 Identities = 36/203 (17%), Positives = 82/203 (40%), Gaps = 7/203 (3%)

Query: 12  FSPEGRLYQVEYAM-EAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDD 70
           +     L +  +   +A     + +G+   +GVV+  + + T   +    +  K+++I  
Sbjct: 9   YQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISP 68

Query: 71  HVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPF 130
            + CA AG  +D   +        + ++        V   +Q L      Y         
Sbjct: 69  KIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQG-----HI 123

Query: 131 GVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQ 190
           G   + AG D   G  L+     G+       ++G+ + AA ++L+  +K D+++EEA++
Sbjct: 124 GAYLIVAGVDPT-GSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIK 182

Query: 191 LALKVLSKTMDSTSLTSDKLELA 213
           LA   +   + +   +   +++ 
Sbjct: 183 LASDAIQAGIWNDLGSGSNVDVC 205

>1ryp_I 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1g0u_H* 1jd2_H* 1g65_H 1vsy_I 1z7q_I 2f16_H* 2fak_H* 2fny_H* 2gpl_H* 3d29_H* 3dy3_H* 3dy4_H* 3e47_H* 3gpj_H* 3gpt_H* 3gpw_H* 3hye_H* 3l5q_M 3mg0_H* 3mg4_H* ... Length = 222

 Score =  161 bits (409), Expect = 2e-49
 Identities = 34/181 (18%), Positives = 76/181 (41%), Gaps = 6/181 (3%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +G+   +GVV+  + + T   +    +  K+++I   + CA AG  +D   +      
Sbjct: 2   TIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGS 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
             + ++        V   +Q L      Y         G   + AG D   G  L+    
Sbjct: 62  NIELHSLYTSREPRVVSALQMLKQHLFKYQG-----HIGAYLIVAGVDPT-GSHLFSIHA 115

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLEL 212
            G+       ++G+ + AA ++L+  +K D+++EEA++LA   +   + +   +   +++
Sbjct: 116 HGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDV 175

Query: 213 A 213
            
Sbjct: 176 C 176

>1iru_I 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_H* 3une_H Length = 234

 Score =  160 bits (407), Expect = 4e-49
 Identities = 33/183 (18%), Positives = 76/183 (41%), Gaps = 6/183 (3%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           +  G++ KDG+VL  + + T  ++    +  K++ I  ++ C  AG  +D ++       
Sbjct: 2   TIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISS 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
             + ++ +      V    + L      Y  +      G + +  G D   G  LY   P
Sbjct: 62  NLELHSLSTGRLPRVVTANRMLKQMLFRYRGY-----IGAALVLGGVDVT-GPHLYSIYP 115

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLEL 212
            G+        +G+ + AA ++ +  ++ D+  EEA  L  + ++  + +   +   ++L
Sbjct: 116 HGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDL 175

Query: 213 AEV 215
             +
Sbjct: 176 CVI 178

>1q5q_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, RH erythropolis, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4 Length = 235

 Score =  148 bits (375), Expect = 2e-44
 Identities = 50/229 (21%), Positives = 92/229 (40%), Gaps = 11/229 (4%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + + +  K GV+L G+++ T   L  S   EK+Y  D++ A  +AG    A  L+    V
Sbjct: 2   TIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAV 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGY----TQFGGLRPFGVSFLFAGWDKNYGFQLY 148
           + + Y      P+  +     L    +G      Q   + P  V +     D++   ++ 
Sbjct: 62  ELEHYEKIEGVPLTFDGKANRLASMVRGNLGAAMQGLAVVPLLVGYDLDADDESRAGRIV 121

Query: 149 MSDPSGNYGGWKA--AAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLT 206
             D  G     +A   A+G+ +  A+S LK+ Y  D   E A++ A++ L    D  S T
Sbjct: 122 SYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSDEETALRAAIESLYDAADDDSAT 181

Query: 207 -----SDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQPAAETS 250
                +  +    V +  +G V     +   L++ +V     Q  +   
Sbjct: 182 GGPDLTRGIYPTAVTITQAGAVHVSEETTSELARRIVAERTEQGGSARH 230

>1yar_H Proteasome beta subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase-HYD activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_H 1yau_H 3ipm_H 1pma_B 3jrm_H 3c92_H 3c91_H 3jse_H 3jtl_H Length = 217

 Score =  143 bits (362), Expect = 1e-42
 Identities = 38/190 (20%), Positives = 86/190 (45%), Gaps = 6/190 (3%)

Query: 26  EAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANI 85
           + +    + +GI  KD V++  E++VT +      + +K+++ID +    +AG++ DA +
Sbjct: 3   QTLETGTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQV 62

Query: 86  LINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGF 145
           L+   + + + Y    +  MP+E +   L +            P+ V  L  G D     
Sbjct: 63  LVRYMKAELELYRLQRRVNMPIEAVATLLSNMLNQVKY----MPYMVQLLVGGIDT--AP 116

Query: 146 QLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSL 205
            ++  D +G       A+ G+ +     +L+  Y + ++ +E V L ++ +S      S 
Sbjct: 117 HVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQRDSA 176

Query: 206 TSDKLELAEV 215
           +   +++A +
Sbjct: 177 SGGMIDVAVI 186

>1q5r_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, hydrolase; 3.10A {Rhodococcus erythropolis} SCOP: d.153.1.4 PDB: 2h6j_H Length = 294

 Score =  128 bits (323), Expect = 5e-36
 Identities = 44/204 (21%), Positives = 83/204 (40%), Gaps = 8/204 (3%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
            ++R    S   R      + +   +  + + +  K GV+L G+++ T   L  S   E 
Sbjct: 39  PENRIGHRSHSTRGGDGMESGDLAPHGTTIVALTYKGGVLLAGDRRATQGNLIASRDVEA 98

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +Y  D++ A  +AG    A  L+    V+ + Y      P+  +     L    +G    
Sbjct: 99  VYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKANRLASMVRGN-LG 157

Query: 125 GGLRPFGVSFLFAGWD-----KNYGFQLYMSDPSGNYGGWKA--AAIGANNQAAQSILKQ 177
             ++   V  L  G+D     ++   ++   D  G     +A   A+G+ +  A+S LK+
Sbjct: 158 AAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKK 217

Query: 178 DYKDDISREEAVQLALKVLSKTMD 201
            Y  D   E A++ A++ L    D
Sbjct: 218 IYSPDSDEETALRAAIESLYDAAD 241

>3nzj_K Proteasome component PRE2; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_K* 3nzx_K* Length = 287

 Score =  124 bits (312), Expect = 2e-34
 Identities = 29/176 (16%), Positives = 67/176 (38%), Gaps = 4/176 (2%)

Query: 26  EAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANI 85
             I +  + +    + G+++  + + T+     S + +K+ +I+  +   +AG  +D   
Sbjct: 70  IKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQF 129

Query: 86  LINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGF 145
                  Q + +    +E + V    + L +    Y          +  +  G+ +  G 
Sbjct: 130 WETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGA----GLSMGTMICGYTRKEGP 185

Query: 146 QLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMD 201
            +Y  D  G         +G+    A  +L  +YK D+S E+A+ L  + +     
Sbjct: 186 TIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAH 241

>1ryp_L 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_L 1vsy_L 1z7q_L 3l5q_P 1g65_K* 1g0u_K* 1jd2_K* 2f16_K* 2fak_K* 2fny_K* 2gpl_K* 2zcy_K* 3bdm_K* 3d29_K* 3dy3_K* 3dy4_K* 3e47_K* 3gpj_K* 3gpt_K* 3gpw_K* ... Length = 212

 Score =  118 bits (299), Expect = 3e-33
 Identities = 27/169 (15%), Positives = 65/169 (38%), Gaps = 4/169 (2%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +    + G+++  + + T+     S + +++ +I+  +   +AG  +D          
Sbjct: 2   TTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGS 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           Q + +    +E + V    + L +    Y          +  +  G+ +  G  +Y  D 
Sbjct: 62  QCRLHELREKERISVAAASKILSNLVYQYKGA----GLSMGTMICGYTRKEGPTIYYVDS 117

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMD 201
            G         +G+    A  +L  +YK D+S E+A+ L  + +     
Sbjct: 118 DGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAH 166

>1iru_L 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_K* 3une_K 3unf_K* 3unh_K Length = 204

 Score =  117 bits (295), Expect = 1e-32
 Identities = 33/169 (19%), Positives = 70/169 (41%), Gaps = 5/169 (2%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +    + GV++  + + T+     S + +K+ +I+ ++   +AG  +D +        
Sbjct: 2   TTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLAR 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           Q + Y    +E + V    + L +    Y          +  +  GWDK  G  LY  D 
Sbjct: 62  QCRIYELRNKERISVAAASKLLANMVYQYKGM----GLSMGTMICGWDKR-GPGLYYVDS 116

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMD 201
            GN       ++G+ +  A  ++ + Y  D+  E+A  LA + + +   
Sbjct: 117 EGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATY 165

>2jay_A Proteasome; hydrolase; 1.99A {Mycobacterium tuberculosis} PDB: 3mka_C 3mi0_C* 2fhg_H* 2fhh_H 3krd_C* 3mfe_G 3hfa_H* 3h6i_C 3h6f_C 3hf9_H 3mfe_H Length = 291

 Score =  117 bits (295), Expect = 5e-32
 Identities = 33/176 (18%), Positives = 70/176 (39%), Gaps = 8/176 (4%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + + +    GVV+ G+++ T   + +     K+Y  DD+ A  +AG  + A        V
Sbjct: 59  TIVALKYPGGVVMAGDRRSTQGNMISGRDVRKVYITDDYTATGIAGTAAVAVEFARLYAV 118

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNY-----GFQL 147
           + + Y      P+     +  L    +G       +      L AG+D +        ++
Sbjct: 119 ELEHYEKLEGVPLTFAGKINRLAIMVRGNLAAAM-QGLLALPLLAGYDIHASDPQSAGRI 177

Query: 148 YMSDPSGNY--GGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMD 201
              D +G +        A+G+ +  A+S +K+ Y      +  +++A++ L    D
Sbjct: 178 VSFDAAGGWNIEEEGYQAVGSGSLFAKSSMKKLYSQVTDGDSGLRVAVEALYDAAD 233

>1j2q_H Proteasome beta subunit; ubiquitin, CP, hydrolase; HET: CIB; 2.83A {Archaeoglobus fulgidus} SCOP: d.153.1.4 Length = 202

 Score =  111 bits (280), Expect = 2e-30
 Identities = 46/170 (27%), Positives = 77/170 (45%), Gaps = 6/170 (3%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +G++ KDGVV+  EK+ T      S + +K+Y+I D +A   AG + DA  L    ++
Sbjct: 2   TTVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKI 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           +A  Y    +    V  +     +    Y  F    P+ V  L  G D   G  +Y  DP
Sbjct: 62  EANLYEIRRERKPTVRAIATLTSNLLNSYRYF----PYLVQLLIGGIDSE-GKSIYSIDP 116

Query: 153 SGN-YGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMD 201
            G         A G+ +  A  +L+  +  +I  +EAV+LA++ +   M 
Sbjct: 117 IGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVELAVRAIYSAMK 166

>1ryp_H 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 3nzj_N* 3nzw_N* 3nzx_N* 1vsy_H 3l5q_B 1g65_N* 1fnt_H 1g0u_N* 1jd2_N* 1z7q_H 2f16_N* 2fak_N* 2fny_N* 2gpl_N* 2zcy_N* 3bdm_N* 3d29_N* 3dy3_N* 3dy4_N* 3e47_N* ... Length = 205

 Score =  104 bits (263), Expect = 6e-28
 Identities = 35/207 (16%), Positives = 83/207 (40%), Gaps = 13/207 (6%)

Query: 32  GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTAR 91
            S + +  KDGV+L  + + T+     +  T+K+ ++ D + C  +G  +D   + +  +
Sbjct: 10  ASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQ 69

Query: 92  VQAQRYTYAYQEPMPVE--QLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYM 149
              + YT  Y  P       + + LC        +          + AG+D     ++Y 
Sbjct: 70  YHLELYTSQYGTPSTETAASVFKELC--------YENKDNLTAGIIVAGYDDKNKGEVYT 121

Query: 150 SDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDK 209
               G+      A  G+ +        +++++++S+EE V      LS+ +     +   
Sbjct: 122 IPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQAIKWDGSSGGV 181

Query: 210 LELAEVFLMPSGKVKYQVCSPEALSKL 236
           + +    ++ +  V+  +  P+   +L
Sbjct: 182 IRMV---VLTAAGVERLIFYPDEYEQL 205

>1iru_H 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_N* 3une_N Length = 205

 Score =  103 bits (259), Expect = 2e-27
 Identities = 33/169 (19%), Positives = 64/169 (37%), Gaps = 5/169 (2%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + + +    GVVL  + + T+     +  T+K+  I D + C  +G  +D   + +    
Sbjct: 2   TIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTY 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           Q   ++    EP  V        +    Y +           + AGWD   G Q+Y    
Sbjct: 62  QLGFHSIELNEPPLVHTAASLFKEMCYRYRE-----DLMAGIIIAGWDPQEGGQVYSVPM 116

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMD 201
            G       A  G+ +      +   Y++ +++EE +Q     L+  M+
Sbjct: 117 GGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAME 165

>3unf_N Proteasome subunit beta type-9; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_N Length = 199

 Score =  100 bits (252), Expect = 2e-26
 Identities = 31/207 (14%), Positives = 75/207 (36%), Gaps = 15/207 (7%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + + +    GVV+  + +V++     +   +K+  +   + CA++G  +DA  + + A  
Sbjct: 2   TIMAVEFDGGVVVGSDSRVSAGTAVVNRVFDKLSPLHQRIFCALSGSAADAQAIADMAAY 61

Query: 93  QAQRYTYAYQEPMPVE---QLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYM 149
           Q + +    +EP  V     +V+++    +               + AGWD+        
Sbjct: 62  QLELHGLELEEPPLVLAAANVVKNISYKYRE--------DLLAHLIVAGWDQR-EGGQVY 112

Query: 150 SDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDK 209
               G          G+ +      +   YK  ++ EE  +     ++  M+    +   
Sbjct: 113 GTMGGMLIRQPFTIGGSGSSYIYGYVDAAYKPGMTPEECRRFTTNAITLAMNRDGSSGGV 172

Query: 210 LELAEVFLMPSGKVKYQVCSPEALSKL 236
                +  + +  V ++V   + L K 
Sbjct: 173 ---IYLVTITAAGVDHRVILGDELPKF 196

>1ryp_K 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_K 1g0u_J* 1jd2_J* 1g65_J 1vsy_K 1z7q_K 2f16_J* 2fak_J* 2fny_J* 2gpl_J* 2zcy_J* 3bdm_J* 3d29_J* 3dy3_J* 3dy4_J* 3e47_J* 3gpj_J* 3gpt_J* 3gpw_J* 3hye_J* ... Length = 198

 Score =  100 bits (252), Expect = 2e-26
 Identities = 35/166 (21%), Positives = 61/166 (36%), Gaps = 3/166 (1%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
             +GI  +D V+L   K VT  +     S +K  ++  H   + AG   D        + 
Sbjct: 3   IILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQA 62

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDK-NYGFQLYMSD 151
             Q Y+      +  + +   +        +     P+ V+ L  G+DK     +LY  D
Sbjct: 63  NIQLYSIREDYELSPQAVSSFVRQELAKSIRSRR--PYQVNVLIGGYDKKKNKPELYQID 120

Query: 152 PSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLS 197
             G        A G +     S+L   Y+ D++ EE + L    + 
Sbjct: 121 YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQ 166

>1ryp_M 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_M* 1jd2_L* 1g65_L 1vsy_M 1z7q_M 2f16_L* 2fak_L* 2fny_L* 2gpl_L* 3d29_L* 3dy3_L* 3dy4_L* 3e47_L* 3gpj_L* 3gpt_L* 3gpw_L* 3hye_L* 3l5q_Q 3mg0_L* 3mg4_L* ... Length = 222

 Score = 99.3 bits (248), Expect = 1e-25
 Identities = 35/190 (18%), Positives = 71/190 (37%), Gaps = 22/190 (11%)

Query: 30  NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINT 89
           N G+ +GI  +D  VL G+ +  +     S    K++   D++  +  G  +D + L+  
Sbjct: 8   NGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKR 67

Query: 90  ARVQAQRYTYAYQE-PMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLY 148
            +   + Y + + +  + +    +++     G   F    P+ V  + AG D++    +Y
Sbjct: 68  FKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKRFF----PYYVHTIIAGLDEDGKGAVY 123

Query: 149 MSDPSGNYGGWKAAAIGANNQAAQSILKQDYK-----------------DDISREEAVQL 191
             DP G+Y   +  A GA        L                        +S EE ++L
Sbjct: 124 SFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKL 183

Query: 192 ALKVLSKTMD 201
                +   +
Sbjct: 184 VRDSFTSATE 193

>1iru_K 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_J* 3une_J 3unf_J* 3unh_J Length = 201

 Score = 97.3 bits (243), Expect = 4e-25
 Identities = 40/165 (24%), Positives = 61/165 (36%), Gaps = 2/165 (1%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
             IGI   D V++  ++   S ++Q     +KM+K+ + +     G   D        + 
Sbjct: 3   YLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQK 62

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
             Q Y       +                 +     P+ V+ L AG+D++ G  LY  D 
Sbjct: 63  NVQLYKMRNGYELSPTAAANFTRRNLADCLRSRT--PYHVNLLLAGYDEHEGPALYYMDY 120

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLS 197
                    AA G       SIL + Y   ISRE AV+L  K L 
Sbjct: 121 LAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLE 165

>1iru_J 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_I* 3une_I 3unf_I* 3unh_I Length = 205

 Score = 97.2 bits (243), Expect = 5e-25
 Identities = 21/174 (12%), Positives = 62/174 (35%), Gaps = 6/174 (3%)

Query: 30  NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINT 89
           N G+ + +  K+ V +  +++   +    +T  +K++ + D +   +AG+ +D   +   
Sbjct: 7   NGGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQR 66

Query: 90  ARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWD-KNYGFQLY 148
            + +   Y       +    L+  + +            P+    + AG D K +   + 
Sbjct: 67  LKFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFG----PYYTEPVIAGLDPKTFKPFIC 122

Query: 149 MSDPSGN-YGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMD 201
             D  G           G   +    + +  ++ ++  +   +   + +   +D
Sbjct: 123 SLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVD 176

>1iru_M 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_L* 3une_L 3unf_L* 3unh_L Length = 213

 Score = 96.5 bits (241), Expect = 1e-24
 Identities = 30/180 (16%), Positives = 69/180 (38%), Gaps = 19/180 (10%)

Query: 30  NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINT 89
           N G+ + I  +D  ++  + +++      +  + K YK+ D      +G   D   L   
Sbjct: 8   NGGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKI 67

Query: 90  ARVQAQRYTYAYQEPMPVE---QLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQ 146
              + + Y ++  + M       ++ ++  +++ +       P+ V  +  G D+     
Sbjct: 68  IEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFF-------PYYVYNIIGGLDEEGKGA 120

Query: 147 LYMSDPSGNYGGWKAAAIGANNQAAQSIL---------KQDYKDDISREEAVQLALKVLS 197
           +Y  DP G+Y      A G+ +   Q +L         +      +S + A++L   V  
Sbjct: 121 VYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFI 180

>1ryp_J 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_I* 1g65_I 1vsy_J 2f16_I* 2fak_I* 2fny_I* 2gpl_I* 3d29_I* 3dy3_I* 3dy4_I* 3e47_I* 3gpj_I* 3gpt_I* 3gpw_I* 3hye_I* 3l5q_N 3mg0_I* 3mg4_I* 3oeu_I* 3oev_I* ... Length = 204

 Score = 94.6 bits (236), Expect = 6e-24
 Identities = 32/174 (18%), Positives = 62/174 (35%), Gaps = 7/174 (4%)

Query: 30  NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINT 89
           N G  + +  KD V +  + ++ S+ L  S   EK++    HV   + G+ +D   L   
Sbjct: 7   NGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHY-GHVFLGITGLATDVTTLNEM 65

Query: 90  ARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGF-QLY 148
            R +   Y    +  +  E   Q +  +           P+ V  + AG +   G   + 
Sbjct: 66  FRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFG----PYFVGPVVAGINSKSGKPFIA 121

Query: 149 MSDPSGNYGGWKA-AAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMD 201
             D  G     K     G  +     + +  Y+ ++  E+  +   + L    D
Sbjct: 122 GFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAAD 175

>1g0u_M Proteasome component PRE4; ubiquitin, degradation, protease, NTN-hydrolase; 2.40A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 2zcy_M* 3bdm_M* 3mg6_M* 3mg7_M* 3mg8_M* 3nzj_M* 3nzw_M* 3nzx_M* Length = 266

 Score = 89.4 bits (222), Expect = 2e-21
 Identities = 25/185 (13%), Positives = 60/185 (32%), Gaps = 18/185 (9%)

Query: 25  MEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDAN 84
            + I    S I +   +GV++  +   +   L      E++  + D+    ++G +SD  
Sbjct: 35  QQPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQ 94

Query: 85  ILINTARVQAQRYTYAYQ-----EPMPVE---QLVQSLCDTKQGYTQFGGLRPFGVSFLF 136
            +    +       Y        E +      + + ++      Y +   + P   + + 
Sbjct: 95  HIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVM-----YQRRSKMNPLWNAIIV 149

Query: 137 AGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDD-----ISREEAVQL 191
           AG   N    L   +  G        A G     A  +L++    +      + + A + 
Sbjct: 150 AGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEA 209

Query: 192 ALKVL 196
            +  +
Sbjct: 210 IVNAM 214

>1ryp_N 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_N* 1jd2_M* 1g65_M 1vsy_N 1z7q_N 2f16_M* 2fak_M* 2fny_M* 2gpl_M* 3d29_M* 3dy3_M* 3dy4_M* 3e47_M* 3gpj_M* 3gpt_M* 3gpw_M* 3hye_M* 3l5q_R 3mg0_M* 3mg4_M* ... Length = 233

 Score = 87.8 bits (218), Expect = 3e-21
 Identities = 25/186 (13%), Positives = 60/186 (32%), Gaps = 18/186 (9%)

Query: 25  MEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDAN 84
            + I    S I +   +GV++  +   +   L      E++  + D+    ++G +SD  
Sbjct: 2   QQPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQ 61

Query: 85  ILINTARVQAQRYTYAYQ-----EPMPVE---QLVQSLCDTKQGYTQFGGLRPFGVSFLF 136
            +    +       Y        E +      + + ++      Y +   + P   + + 
Sbjct: 62  HIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVM-----YQRRSKMNPLWNAIIV 116

Query: 137 AGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDD-----ISREEAVQL 191
           AG   N    L   +  G        A G     A  +L++    +      + + A + 
Sbjct: 117 AGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEA 176

Query: 192 ALKVLS 197
            +  + 
Sbjct: 177 IVNAMR 182

>1iru_N 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_M* 3une_M 3unf_M* 3unh_M Length = 219

 Score = 81.5 bits (202), Expect = 5e-19
 Identities = 24/169 (14%), Positives = 52/169 (30%), Gaps = 6/169 (3%)

Query: 32  GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTAR 91
            S +G+  + GVV+  +   +   L    +  ++ ++++      +G  +D   L     
Sbjct: 9   TSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLG 68

Query: 92  VQAQRYTYAY-QEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMS 150
                              +   L              P   + +  G+       L   
Sbjct: 69  QMVIDEELLGDGHSYSPRAIHSWLTRAMYSRRSKMN--PLWNTMVIGGYADG-ESFLGYV 125

Query: 151 DPSGNYGGWKAAAIGANNQAAQSILKQDYKD--DISREEAVQLALKVLS 197
           D  G      + A G     AQ +L++  +    +S+ EA  L  + + 
Sbjct: 126 DMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMR 174

>1g3k_A ATP-dependent protease HSLV; hydrolase; 1.90A {Haemophilus influenzae} SCOP: d.153.1.4 PDB: 1g3i_G 1jjw_A 1kyi_G* 1ofh_G* 1ofi_G* 1e94_A* 1g4a_B* 1g4b_M 1hqy_A* 1ht1_C* 1ht2_A* 1ned_A Length = 174

 Score = 45.7 bits (108), Expect = 2e-06
 Identities = 22/162 (13%), Positives = 52/162 (32%), Gaps = 11/162 (6%)

Query: 35  IGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDH-VACAVAGIMSDANILINTARVQ 93
           + +     VV+ G+ +V+        +  K+ ++ +  V    AG  +DA  L      +
Sbjct: 4   VSVRRNGQVVVGGDGQVSLGNTVMKGNARKVRRLYNGKVLAGFAGGTADAFTL--FELFE 61

Query: 94  AQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPS 153
            +   +         +L +     +        LR      + A   ++           
Sbjct: 62  RKLEMHQGHLLKSAVELAKDWRTDRA-------LRKLEAMLIVADEKESLIITGIGDVVQ 114

Query: 154 GNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKV 195
                  A   G N   + +    +   ++S  E V+ +L++
Sbjct: 115 PEEDQILAIGSGGNYALSAARALVEN-TELSAHEIVEKSLRI 155

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	250
1iru_C	261	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_C	244	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_A	243	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_E	241	20S proteasome; cell cycle, immune response, prote	100.0
1iru_G	254	20S proteasome; cell cycle, immune response, prote	100.0
1iru_A	246	20S proteasome; cell cycle, immune response, prote	100.0
1iru_D	248	20S proteasome; cell cycle, immune response, prote	100.0
1yar_A	233	Proteasome alpha subunit; proteasome 20S, PA26 pro	100.0
1ryp_D	241	20S proteasome; multicatalytic proteinase, protein	100.0
3h4p_A	264	Proteasome subunit alpha; core particle, cytoplasm	100.0
1j2p_A	246	Alpha-ring, proteasome alpha subunit; hydrolase; 2	100.0
1ryp_B	250	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_B	233	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_E	242	20S proteasome; multicatalytic proteinase, protein	100.0
3nzj_F	288	Proteasome component C1; ubiquitin, protein degrad	100.0
1iru_F	263	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_G	244	20S proteasome; multicatalytic proteinase, protein	100.0
1ryp_F	233	20S proteasome; multicatalytic proteinase, protein	100.0
1q5q_A	259	Proteasome alpha-type subunit 1; proteasome assemb	100.0
3mi0_A	248	Proteasome subunit alpha; enzyme inhibitors, lacto	100.0
3h4p_a	219	Proteasome subunit beta; core particle, cytoplasm,	100.0
1yar_H	217	Proteasome beta subunit; proteasome 20S, PA26 prot	100.0
1j2q_H	202	Proteasome beta subunit; ubiquitin, CP, hydrolase;	100.0
1q5r_H	294	Proteasome beta-type subunit 1; proteasome assembl	100.0
3nzj_K	287	Proteasome component PRE2; ubiquitin, protein degr	100.0
2jay_A	291	Proteasome; hydrolase; 1.99A {Mycobacterium tuberc	100.0
1iru_L	204	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_L	212	20S proteasome; multicatalytic proteinase, protein	100.0
1q5q_H	235	Proteasome beta-type subunit 1; proteasome assembl	100.0
1iru_H	205	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_N	233	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_N	219	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_H	205	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_M	213	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_K	198	20S proteasome; multicatalytic proteinase, protein	100.0
1g0u_M	266	Proteasome component PRE4; ubiquitin, degradation,	100.0
3unf_H	234	Proteasome subunit beta type-10; antigen presentat	100.0
1iru_J	205	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_J	204	20S proteasome; multicatalytic proteinase, protein	100.0
3nzj_H	261	Proteasome component PUP1; ubiquitin, protein degr	100.0
1ryp_M	222	20S proteasome; multicatalytic proteinase, protein	100.0
3unf_N	199	Proteasome subunit beta type-9; antigen presentati	100.0
1iru_K	201	20S proteasome; cell cycle, immune response, prote	100.0
1ryp_I	222	20S proteasome; multicatalytic proteinase, protein	100.0
1iru_I	234	20S proteasome; cell cycle, immune response, prote	100.0
2z3b_A	180	ATP-dependent protease HSLV; N-terminal nucleophIl	100.0
1m4y_A	171	ATP-dependent protease HSLV; N-terminal catalytic	100.0
1g3k_A	174	ATP-dependent protease HSLV; hydrolase; 1.90A {Hae	100.0

>1iru_C 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_B* 3une_B 3unf_B* 3unh_B

Probab=100.00  E-value=1.2e-64  Score=433.92  Aligned_cols=246  Identities=59%  Similarity=0.971  Sum_probs=233.1

Q ss_pred             CCCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         1 ~~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      |+++||+++|+|||||||||||||++|+.+|+|+|||+++||||||+|+|.++|+++.+++.+||++|+++++|+++|..
T Consensus         1 m~~~yd~~~t~fsp~Grl~QvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r~~~g~~~~~~~~~KI~~i~~~i~~~~aG~~   80 (261)
T 1iru_C            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNEDMACSVAGIT   80 (261)
T ss_dssp             -CTTTCCCTTCCCTTSCCHHHHHHHHHHTTSCCEEEEBCSSEEEEEECCCCCCTTBCCCSSCSSEEECSSSEEEEEEECH
T ss_pred             CCCccCCCCccCCCCCeehHHHhHHHHHhcCCcEEEEEeCCEEEEEEecccCCcccccCCCCccEEEecCCEEEEEeEcH
Confidence            89999999999999999999999999999999999999999999999999999999988778999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce
Q 025640           81 SDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK  160 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~  160 (250)
                      +|++.+.+.++.++..|++.++.+++++.+++.+++++|.|+++.+.|||+|++||||||+..||+||.+||.|++.+++
T Consensus        81 aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~  160 (261)
T 1iru_C           81 SDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWK  160 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCEEEEEEEEETTTEEEEEEEETTTEEEECS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcCcceEEEEEEEEeCCCCcEEEEECCCceEEeee
Confidence            99999999999999999999999999999999999999999999899999999999999976689999999999999999


Q ss_pred             EEEEeCChHHHHHHHHhhCCC-CCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          161 AAAIGANNQAAQSILKQDYKD-DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       161 ~~a~G~g~~~~~~~L~~~~~~-~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      ++|+|+|+.+++++|++.|++ +||++||++++++||..+.+++..++++++|++|++++. ...|++++++||+.++..
T Consensus       161 ~~aiGsgs~~a~~~Le~~~~~~~ms~eeA~~la~~al~~~~~~d~~sg~~i~v~vi~~~~~-~~~~~~l~~~ei~~~l~~  239 (261)
T 1iru_C          161 ATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENG-KTVIRVLKQKEVEQLIKK  239 (261)
T ss_dssp             EEEESTTTTHHHHHHHHHCCTTCCCHHHHHHHHHHHHHHSSSCTTCCSTTCEEEEEECCSS-SCEEEECCHHHHHHHHHH
T ss_pred             eEEeCcccHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEEcCCC-eeeEEECCHHHHHHHHHH
Confidence            999999999999999999999 999999999999999999999999999999999999862 224899999999999999


Q ss_pred             hCCCCccc
Q 025640          240 HGVTQPAA  247 (250)
Q Consensus       240 ~~~~~~~~  247 (250)
                      +.+.+.++
T Consensus       240 ~~~~~~~~  247 (261)
T 1iru_C          240 HEEEEAKA  247 (261)
T ss_dssp             HHTTTTTT
T ss_pred             HHhchhhh
Confidence            86544433

>1ryp_C 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_B* 1g65_B 2f16_B* 2fak_B* 2fny_B* 2gpl_B* 3d29_B* 3dy3_B* 3dy4_B* 3e47_B* 3gpj_B* 3gpt_B* 3gpw_B* 3hye_B* 3mg0_B* 3mg4_B* 3okj_B* 3shj_B* 3tdd_B* 3nzj_B* ...

Probab=100.00  E-value=5.6e-63  Score=419.78  Aligned_cols=240  Identities=60%  Similarity=0.994  Sum_probs=228.3

Q ss_pred             CCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchH
Q 025640            2 SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMS   81 (250)
Q Consensus         2 ~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~   81 (250)
                      +|+||+++|+|||||||+|||||.+|+.+|+|+|||+++||||||+|+|.++++++.+++.+||++|+++++|+++|..+
T Consensus         2 ~~~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~a   81 (244)
T 1ryp_C            2 SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTA   81 (244)
T ss_dssp             CGGGCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECSSCCSSBCSTTCCSSEEESSSSEEEEEEECHH
T ss_pred             CCccCCCCceECcCCeeHHHHhHHHHHhcCCcEEEEEeCCEEEEEEeeccCCcCccCCCCCCcEEEECCCEEEEEEEcHH
Confidence            57899999999999999999999999999999999999999999999999999988667899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceE
Q 025640           82 DANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKA  161 (250)
Q Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~  161 (250)
                      |++.+.+.++.++..|++.++.+++++.+++.+++++|.|+++.+.|||++++||||||+.++|+||.+||.|++.++++
T Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~  161 (244)
T 1ryp_C           82 DAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKA  161 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCCEEEEEEEEETTTEEEEEEECTTCCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccceEEEEEEEEEcCCCCCEEEEECCCccEEeeeE
Confidence            99999999999999999999999999999999999999999999999999999999999546999999999999999999


Q ss_pred             EEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEE--eCCCCceeEEECCHHHHHHHHHH
Q 025640          162 AAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVF--LMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       162 ~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~--~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      +|+|+|+.+++++||+.|+++|+++||++++++||..+.+++..++++++|++|+  +++. ...|+.++++||+.++..
T Consensus       162 ~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~rd~~sg~~i~v~vi~~~~~~~-~~~~~~l~~~ei~~~~~~  240 (244)
T 1ryp_C          162 ISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDG-EVYQKIFKPQEIKDILVK  240 (244)
T ss_dssp             EEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSSSSCCGGGEEEEEEECCSSSS-SCEEEECCHHHHHHHHHH
T ss_pred             EEECCCcHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHhccccCCCCcEEEEEEEeecCCC-ceeEEECCHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999867789999999999  8862 124899999999999998


Q ss_pred             hCC
Q 025640          240 HGV  242 (250)
Q Consensus       240 ~~~  242 (250)
                      ++.
T Consensus       241 ~~~  243 (244)
T 1ryp_C          241 TGI  243 (244)
T ss_dssp             HTC
T ss_pred             hhc
Confidence            864

>1ryp_A 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_G* 1g65_G 1vsy_A 2f16_G* 2fak_G* 2fny_G* 2gpl_G* 3d29_G* 3dy3_G* 3dy4_G* 3e47_G* 3gpj_G* 3gpt_G* 3gpw_G* 3hye_G* 3l5q_A 3mg0_G* 3mg4_G* 3oeu_G* 3oev_G* ...

Probab=100.00  E-value=1e-62  Score=417.92  Aligned_cols=233  Identities=31%  Similarity=0.508  Sum_probs=222.4

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcC-CccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGN-AGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMS   81 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~-g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~   81 (250)
                      .+||+++|+|||||||||||||.||+++ |+|+|||+++||||||+|+|.+.++ +..++.+||++|+++++|+++|+.+
T Consensus         1 ~~yd~~~t~fsp~Grl~QvEYA~~av~~~Gtt~vgi~~~dgVvlaad~r~~~~l-~~~~~~~Ki~~i~~~i~~~~aG~~a   79 (243)
T 1ryp_A            1 AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKL-LDPTTVSYIFCISRTIGMVVNGPIP   79 (243)
T ss_dssp             CGGGGTSSSCCTTSCCHHHHHHHHHTTTTCCCEEEEECSSEEEEEEECCCCCTT-BCGGGCCSEEECSSSCEEEEESCHH
T ss_pred             CCCCCCCceECCCCeeHHHHHHHHHHhcCCCcEEEEEeCCEEEEEEEecCCccc-cCCCcCCceEEECCCEEEEEEecHH
Confidence            3799999999999999999999999999 9999999999999999999999444 4456889999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceE
Q 025640           82 DANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKA  161 (250)
Q Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~  161 (250)
                      |++.+.+.++.++..|++.++.+++++.+++.+++.+|.|+++++.|||+|++||||||+.+||+||++||+|++.++++
T Consensus        80 D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~l~~y~~~~~~rP~~v~~lvaG~D~~~gp~Ly~~dp~G~~~~~~~  159 (243)
T 1ryp_A           80 DARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKA  159 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSCEEEEEEEETTTEEEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCccccceEEEEEEEcCCCCcEEEEEcCCCCEEEEEE
Confidence            99999999999999999999999999999999999999999998999999999999999866899999999999999999


Q ss_pred             EEEeCChHHHHHHHHhhCCC-------CCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHH
Q 025640          162 AAIGANNQAAQSILKQDYKD-------DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALS  234 (250)
Q Consensus       162 ~a~G~g~~~~~~~L~~~~~~-------~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~  234 (250)
                      +|+|+++++++++||+.|++       +||++||++++++||..+.+|+ .++++++|++|++++     +++++++||+
T Consensus       160 ~a~G~gs~~a~~~Le~~~~~~~~~~~~~ms~eea~~l~~~al~~~~~rd-~s~~~iev~vi~~~g-----~~~l~~~ei~  233 (243)
T 1ryp_A          160 TATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTE-FSKNDLEVGVATKDK-----FFTLSAENIE  233 (243)
T ss_dssp             EEESTTHHHHHHHHHHHHHHHCSSSCCCSSHHHHHHHHHHHHHHHHTCC-CCTTSEEEEEEETTE-----EEECCHHHHH
T ss_pred             EEECCCcHHHHHHHHHHhhhcccccccCCCHHHHHHHHHHHHHHHhccc-CCCCcEEEEEEECCC-----eEECCHHHHH
Confidence            99999999999999999998       9999999999999999999988 789999999999986     8999999999


Q ss_pred             HHHHHhCC
Q 025640          235 KLLVKHGV  242 (250)
Q Consensus       235 ~~~~~~~~  242 (250)
                      .++..+.+
T Consensus       234 ~~~~~~~~  241 (243)
T 1ryp_A          234 ERLVAIAE  241 (243)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHHhhc
Confidence            99998844

>1iru_E 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_D* 3une_D 3unf_D* 3unh_D

Probab=100.00  E-value=2.5e-62  Score=415.09  Aligned_cols=232  Identities=38%  Similarity=0.656  Sum_probs=220.4

Q ss_pred             CCC-CCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCc
Q 025640            1 MSR-RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGI   79 (250)
Q Consensus         1 ~~~-~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~   79 (250)
                      |+| +||+++|+|||||||+|||||.+|+.+|+|+|||+++||||||+|+|.++|+++ +++.+||++|+++++|+++|.
T Consensus         3 m~~~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~-~~~~~Ki~~i~~~i~~~~aG~   81 (241)
T 1iru_E            3 LTRSEYDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME-PSSIEKIVEIDAHIGCAMSGL   81 (241)
T ss_dssp             -----CCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECCCCCTTBC-TTSCCSEEEEETTEEEEEEEC
T ss_pred             CccCCCCCCCceECCCCccHHHHHHHHHHHcCCcEEEEEcCCEEEEEEecccCCcCcC-ccccceEEEEcCCEEEEEeeC
Confidence            677 899999999999999999999999999999999999999999999999999988 678999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCC-----CcceeEEEEEEEEeCCCCeEEEEECCCC
Q 025640           80 MSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGG-----LRPFGVSFLFAGWDKNYGFQLYMSDPSG  154 (250)
Q Consensus        80 ~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~-----~rP~~~~~iv~G~d~~~~~~Ly~vd~~G  154 (250)
                      .+|++.+.+.++.++..|++.++++++++.+++.+++++|.|+++.+     .|||++++||||||+ .||+||.+||.|
T Consensus        82 ~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~y~~~~~~~~l~~rp~~v~~lvaG~D~-~gp~Ly~idp~G  160 (241)
T 1iru_E           82 IADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDE-KGPQLFHMDPSG  160 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBSSCCCEEEEEEEEET-TEEEEEEECTTS
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhccccccccccccceEEEEEEEEeC-CCCEEEEECCCC
Confidence            99999999999999999999999999999999999999999999887     899999999999995 689999999999


Q ss_pred             ceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHH
Q 025640          155 NYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALS  234 (250)
Q Consensus       155 ~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~  234 (250)
                      ++.+++++|+|+|+.+++++||+.|+++||++||++++++||..+.++ ..++++++|++|++++    .+++++++||+
T Consensus       161 ~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~-~~sg~~i~v~vi~~~~----~~~~l~~~ei~  235 (241)
T 1iru_E          161 TFVQCDARAIGSASEGAQSSLQELYHKSMTLKEAIKSSLIILKQVMEE-KLNATNIELATVQPGQ----NFHMFTKEELE  235 (241)
T ss_dssp             CEEEBSEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSS-CCCTTSEEEEEECSSS----CCEECCHHHHH
T ss_pred             cEEecceEEECCCcHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhc-cCCCCCEEEEEEECCC----CeEECCHHHHH
Confidence            999999999999999999999999999999999999999999999998 7889999999999987    38999999999


Q ss_pred             HHHHH
Q 025640          235 KLLVK  239 (250)
Q Consensus       235 ~~~~~  239 (250)
                      .++.+
T Consensus       236 ~~~~~  240 (241)
T 1iru_E          236 EVIKD  240 (241)
T ss_dssp             HHHTT
T ss_pred             HHHHh
Confidence            99864

>1iru_G 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_F* 3une_F 3unf_F* 3unh_F

Probab=100.00  E-value=9.8e-63  Score=420.44  Aligned_cols=240  Identities=33%  Similarity=0.519  Sum_probs=227.7

Q ss_pred             CCCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         1 ~~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      |+.+||+++|+|||||||||||||.+|+++|+|+|||+++||||||+|+|.++|+++. ++.+||++|+++++|+++|..
T Consensus         3 ~~~~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~-~~~~KI~~i~~~i~~~~aG~~   81 (254)
T 1iru_G            3 IGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEE-GSNKRLFNVDRHVGMAVAGLL   81 (254)
T ss_dssp             CCSSTTSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSBEEEEEEEECSCTTBCT-TTTCCEEEEETTEEEEEEECH
T ss_pred             cccccCCCCccCCcCCccHHHHhHHHHHhcCCCEEEEEECCEEEEEEecccCCCCcCc-CcCCcEEEECCCEEEEEecCh
Confidence            5779999999999999999999999999999999999999999999999999999986 588999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce
Q 025640           81 SDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK  160 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~  160 (250)
                      +|++.+.+.++.++..|++.++.+++++.+++.+++++|.|++++++|||+|++||||||+..||+||.+||.|++.+++
T Consensus        82 aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~  161 (254)
T 1iru_G           82 ADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYW  161 (254)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSEEEEEEEEETTTEEEEEEECTTCCEEEBS
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccccccccceEEEEEEEEeCCCCcEEEEEcCCCCEEeee
Confidence            99999999999999999999999999999999999999999999899999999999999955689999999999999999


Q ss_pred             EEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 025640          161 AAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH  240 (250)
Q Consensus       161 ~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~  240 (250)
                      ++|+|+|+.+++++||+.|+++|+++||++++++||+.+.+++..++++++|++|+++..+  .++++++++++.++..+
T Consensus       162 ~~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~~~~~~~~iev~vi~~~~~g--~~~~l~~~~i~~~~~~~  239 (254)
T 1iru_G          162 GCAIGKARQAAKTEIEKLQMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNG--RHEIVPKDIREEAEKYA  239 (254)
T ss_dssp             EEEESTTHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHSCSSSSCCEEEEEEECBTTTTT--CCEECCHHHHHHHHHHH
T ss_pred             eEEecCccHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhhccCCCCcEEEEEEEcCCCC--CeEECCHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999887778999999999987322  38999999999999887


Q ss_pred             CCC
Q 025640          241 GVT  243 (250)
Q Consensus       241 ~~~  243 (250)
                      ++.
T Consensus       240 ~~~  242 (254)
T 1iru_G          240 KES  242 (254)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            643

>1iru_A 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_G* 3une_G 3unf_G* 3unh_G

Probab=100.00  E-value=5.8e-62  Score=414.01  Aligned_cols=237  Identities=32%  Similarity=0.572  Sum_probs=225.0

Q ss_pred             CCC--CCCCCccccCCCCcccccchHHHHhcC-CccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEe
Q 025640            1 MSR--RYDSRTTIFSPEGRLYQVEYAMEAIGN-AGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVA   77 (250)
Q Consensus         1 ~~~--~yd~~~~~f~p~G~l~qveya~~a~~~-g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~s   77 (250)
                      ||+  +||+++|+|||||||+|||||.+|+.+ |+|+|||+++||||||+|+|.+. .++.+++.+||++|+++++|+++
T Consensus         3 m~~~~~yd~~~t~fsp~Grl~QvEya~~av~~~Gtt~vgi~~~dgVvlaaD~r~~~-~l~~~~~~~Ki~~i~~~i~~~~a   81 (246)
T 1iru_A            3 RGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPD-KLLDSSTVTHLFKITENIGCVMT   81 (246)
T ss_dssp             CSCCCTTTTTSSCCCTTSCCHHHHHHHHHHHTTCCEEEEEECSSEEEEEEECCCCC-SSBCGGGCCSEEESSSSCEEEEE
T ss_pred             CCccCCcCCCCccCCCCCeehHHHHHHHHHhcCCCCEEEEEeCCEEEEEEeecCCC-cccCCCccCceEEECCCEEEEEe
Confidence            666  899999999999999999999999999 99999999999999999999995 44555688999999999999999


Q ss_pred             CchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCcee
Q 025640           78 GIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYG  157 (250)
Q Consensus        78 G~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~  157 (250)
                      |..+|++.+.+.++.++..|++.++.+++++.+++.+++++|.|+++.+.|||+|++||||||+.+||+||.+||.|++.
T Consensus        82 G~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~y~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~  161 (246)
T 1iru_A           82 GMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYC  161 (246)
T ss_dssp             ECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSEEEEEEEEETTTEEEEEEECTTSCEE
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCCCCcceEEEEEEEeCCCCeEEEEEcCCeeEE
Confidence            99999999999999999999999999999999999999999999998899999999999999986689999999999999


Q ss_pred             cceEEEEeCChHHHHHHHHhhCCC--CCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHH
Q 025640          158 GWKAAAIGANNQAAQSILKQDYKD--DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSK  235 (250)
Q Consensus       158 ~~~~~a~G~g~~~~~~~L~~~~~~--~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~  235 (250)
                      +++++|+|+|+.+++++||+.|++  +|+++||++++++||..+.+++ .++++++|++|++++   ..|++++++||+.
T Consensus       162 ~~~~~aiG~gs~~a~~~Le~~~~~~~~ms~eea~~la~~al~~~~~rd-~sg~~i~v~vi~~~g---~~~~~l~~~ei~~  237 (246)
T 1iru_A          162 GFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSID-FKPSEIEVGVVTVEN---PKFRILTEAEIDA  237 (246)
T ss_dssp             EBSEEEEETTHHHHHHHHHHHTTSCCCCCHHHHHHHHHHHHHHHTTCC-CCTTSEEEEEEETTE---EEEEECCHHHHHH
T ss_pred             EeeEEEECCCcHHHHHHHHHhhcccCCCCHHHHHHHHHHHHHHHhccc-CCCCcEEEEEEECCC---CeEEECCHHHHHH
Confidence            999999999999999999999999  9999999999999999999998 889999999999986   3489999999999


Q ss_pred             HHHHhCC
Q 025640          236 LLVKHGV  242 (250)
Q Consensus       236 ~~~~~~~  242 (250)
                      ++..+.+
T Consensus       238 ~~~~~~~  244 (246)
T 1iru_A          238 HLVALAE  244 (246)
T ss_dssp             HHHHHHT
T ss_pred             HHHHhhc
Confidence            9998843

>1iru_D 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unf_C* 3une_C* 3unh_C 3unb_C*

Probab=100.00  E-value=1.9e-62  Score=417.38  Aligned_cols=238  Identities=37%  Similarity=0.605  Sum_probs=224.8

Q ss_pred             CCCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         1 ~~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      |+  ||+++|+|||||||||||||++|+++|+|+|||+++||||||+|+|.++++.. .++.+||++|+++++|+++|..
T Consensus         1 ~~--yd~~~t~fsp~Grl~QvEYA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~-~~~~~KI~~i~~~i~~~~aG~~   77 (248)
T 1iru_D            1 MS--YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQD-ERTVRKICALDDNVCMAFAGLT   77 (248)
T ss_dssp             -C--CCCCCSCCCTTSCCHHHHHHHHHHHTSCCEEEECCSSEEEEEECCCCCCSSSC-GGGGCSEEESSSSCEEEEEECH
T ss_pred             CC--ccCCCceECCCCcchHHHHHHHHHHcCCCEEEEEeCCEEEEEEeecccccCcc-CCCCCcEEEEcCCEEEEEeecH
Confidence            77  99999999999999999999999999999999999999999999999999654 4688999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce
Q 025640           81 SDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK  160 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~  160 (250)
                      +|++.+.+.++.++..|++.++++++++.+++.+++++|.|+++.+.|||+|++||||||+.++|+||.+||.|++.+++
T Consensus        78 aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~  157 (248)
T 1iru_D           78 ADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWK  157 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEECSSSCEEEEEECTTSCEEEBS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhccCCcccccEEEEEEEEeCCCCcEEEEEcCCCcEEEee
Confidence            99999999999999999999999999999999999999999999899999999999999955699999999999999999


Q ss_pred             EEEEeCChHHHHHHHHhhCCCCC--CHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 025640          161 AAAIGANNQAAQSILKQDYKDDI--SREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLV  238 (250)
Q Consensus       161 ~~a~G~g~~~~~~~L~~~~~~~~--s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~  238 (250)
                      ++|+|+|+.+++++||+.|+++|  |++||++++++||..+.+   .++++++|++|++++    .|++++++||+.++.
T Consensus       158 ~~aiG~gs~~a~~~Le~~~~~~m~~s~eea~~la~~al~~~~~---~sg~~i~v~vi~~~g----~~~~l~~~ei~~~~~  230 (248)
T 1iru_D          158 ANAIGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKALLEVVQ---SGGKNIELAVMRRDQ----SLKILNPEEIEKYVA  230 (248)
T ss_dssp             EEEESTTHHHHHHHHTTTCCSSTTCSHHHHHHHHHHHHHTTSC---TTSTTCCEEEEESSS----CEECCCHHHHHHHTT
T ss_pred             EEEECCCcHHHHHHHHHhhcccccCCHHHHHHHHHHHHHHHHc---CCCCcEEEEEEECCC----cEEECCHHHHHHHHH
Confidence            99999999999999999999999  999999999999999997   468999999999986    489999999999999


Q ss_pred             HhCCCCcccc
Q 025640          239 KHGVTQPAAE  248 (250)
Q Consensus       239 ~~~~~~~~~~  248 (250)
                      .+.+.+++|.
T Consensus       231 ~~~~~~~~~~  240 (248)
T 1iru_D          231 EIEKEKEENE  240 (248)
T ss_dssp             TTTTTTTTTT
T ss_pred             HHHhcchhhh
Confidence            8876665544

>1yar_A Proteasome alpha subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase-HYD activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_A 1pma_A 3c91_A 3c92_A 3ipm_A 2ku1_A 2ku2_A 1yau_A 3jrm_A 3jse_A 3jtl_A

Probab=100.00  E-value=2.7e-62  Score=412.87  Aligned_cols=230  Identities=39%  Similarity=0.694  Sum_probs=212.0

Q ss_pred             CCC-CCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCc
Q 025640            1 MSR-RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGI   79 (250)
Q Consensus         1 ~~~-~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~   79 (250)
                      |+| +||+++|+|||||||+|||||.+|+++|+|+|||+++||||||+|+|.++++.. +++.+||++|+++++|+++|.
T Consensus         3 m~~~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~~~~-~~~~~Ki~~i~~~i~~~~aG~   81 (233)
T 1yar_A            3 QGQMAYSRAITVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIE-QNSIEKIQLIDDYVAAVTSGL   81 (233)
T ss_dssp             ----------CCCCTTSCCHHHHHHHHHHTTSCCEEEEEETTEEEEEECCCCCCTTBC-STTCCSEEEEETTEEEEEEEB
T ss_pred             cccccCCCCCceECcCCeeHHHHhHHHHHhcCCcEEEEEECCEEEEEEeccCCccccc-ccccCeEEEecCCEEEEEeeC
Confidence            777 899999999999999999999999999999999999999999999999998654 568899999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecc
Q 025640           80 MSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW  159 (250)
Q Consensus        80 ~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~  159 (250)
                      .+|++.+.+.++.++..|++.++.+++++.+++.+++.+|.|+++.+.|||++++||||||+ .||+||.+||.|++.++
T Consensus        82 ~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a~~l~~~~~~~~~~~~~rp~~v~~lvaG~D~-~gp~Ly~id~~G~~~~~  160 (233)
T 1yar_A           82 VADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQ-IGPRLFDCDPAGTINEY  160 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCEEEEEEEECS-SCEEEEEECTTCCEEEB
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCcCcceEEEEEEEEeC-CCCEEEEECCCCCEEee
Confidence            99999999999999999999999999999999999999999999999999999999999998 58999999999999999


Q ss_pred             eEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 025640          160 KAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL  237 (250)
Q Consensus       160 ~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~  237 (250)
                      +++|+|+|+.+++++||+.|+++||++||++++++||..+.+++. ++++++|++|++++    .+++++++||+.++
T Consensus       161 ~~~aiG~gs~~a~~~Le~~~~~~~s~eea~~la~~al~~~~~~d~-s~~~i~v~vi~~~~----~~~~~~~~ei~~~l  233 (233)
T 1yar_A          161 KATAIGSGKDAVVSFLEREYKENLPEKEAVTLGIKALKSSLEEGE-ELKAPEIASITVGN----KYRIYDQEEVKKFL  233 (233)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHTSCSSC-CCCCCEEEEEETTS----CCEECCHHHHHTTC
T ss_pred             eEEEEcCCcHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhccC-CCCcEEEEEEECCC----CEEECCHHHHHhhC
Confidence            999999999999999999999999999999999999999999887 79999999999986    38999999998753

>1ryp_D 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_C* 1g65_C 2f16_C* 2fak_C* 2fny_C* 2gpl_C* 3d29_C* 3dy3_C* 3dy4_C* 3e47_C* 3gpj_C* 3gpt_C* 3gpw_C* 3hye_C* 3mg0_C* 3mg4_C* 3oeu_C* 3oev_C* 3okj_C* 3shj_C* ...

Probab=100.00  E-value=5.6e-62  Score=412.90  Aligned_cols=232  Identities=36%  Similarity=0.595  Sum_probs=223.7

Q ss_pred             CCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHH
Q 025640            4 RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDA   83 (250)
Q Consensus         4 ~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~   83 (250)
                      +||+++|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.++|+++.+++.+||++|+++++|+++|..+|+
T Consensus         1 ~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~   80 (241)
T 1ryp_D            1 GYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFSGLNADS   80 (241)
T ss_dssp             CCCCCCSCCBTTTBCHHHHHHHHHHTTSCCEEEEECSSCEEEEEECCCSSCCBCTTTSCCSEEEEETTEEEEEEECHHHH
T ss_pred             CCCCCceeECCCCcchHHHHHHHHHHcCCCEEEEEeCCEEEEEEeeccCccCccccCCcCcEEEecCCEEEEEeecHHHH
Confidence            69999999999999999999999999999999999999999999999999999988789999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCC-CCeEEEEECCCCceecceEE
Q 025640           84 NILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKN-YGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        84 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~-~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      +.+.+.++.++..|++.++.+++++.+++.+++.+|.++|++++|||++++||||||+. ++|+||.+||.|++.+++++
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~~~~~~~rP~~v~~lvaG~D~~~~gp~Ly~idp~G~~~~~~~~  160 (241)
T 1ryp_D           81 RILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQ  160 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSSTTBCCCSEEEEEEECCTTCCSCEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHccCCCCCCcceeeEEEEEcCCCCCeeEEEECCCCCEEEeeeE
Confidence            99999999999999999999999999999999999999999899999999999999985 68999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhC---CCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          163 AIGANNQAAQSILKQDY---KDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~---~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      |+|+|+.+++++||+.|   +++||++||++++++||..+.+   .++++++|++|++++    .++.++++||+.++..
T Consensus       161 aiG~gs~~a~~~Le~~~~~~~~~ms~eea~~l~~~al~~~~~---~sg~~i~v~vi~~~~----~~~~l~~~ei~~~~~~  233 (241)
T 1ryp_D          161 TIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQ---TGAKNIEITVVKPDS----DIVALSSEEINQYVTQ  233 (241)
T ss_dssp             EESTTHHHHHHHHHTTCCTTSCCCSHHHHHHHHHHHHHHHHC---SCSTTEEEEEEETTT----EEEECCHHHHHHHHHH
T ss_pred             EECCCcHHHHHHHHHhhhcccCCCCHHHHHHHHHHHHHHHhc---CCCCcEEEEEEECCC----cEEECCHHHHHHHHHH
Confidence            99999999999999999   9999999999999999999996   679999999999986    4899999999999998


Q ss_pred             hCC
Q 025640          240 HGV  242 (250)
Q Consensus       240 ~~~  242 (250)
                      +.+
T Consensus       234 ~~~  236 (241)
T 1ryp_D          234 IEQ  236 (241)
T ss_dssp             HTH
T ss_pred             Hhh
Confidence            843

>3h4p_A Proteasome subunit alpha; core particle, cytoplasm, hydrolase, protease, threonine protease; 4.10A {Methanocaldococcus jannaschii}

Probab=100.00  E-value=4.2e-63  Score=424.27  Aligned_cols=239  Identities=42%  Similarity=0.723  Sum_probs=221.2

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      .+||+++|+|||||||||||||.+|+++|+|+|||+++||||||+|+|.++++.. +++.+||++|+++++|+++|..+|
T Consensus        10 ~~yd~~~t~fSp~Grl~QvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r~~~~li~-~~~~~KI~~i~d~i~~~~aG~~aD   88 (264)
T 3h4p_A           10 SAYDRAITVFSPEGRLYQVEYAREAVRRGTTAIGIACKDGVVLAVDRRITSKLVK-IRSIEKIFQIDDHVAAATSGLVAD   88 (264)
T ss_dssp             ------CCCCCSSSSCHHHHHHHHHHHHSCCEEEECCSSEEEEEEECCCCSTTBC-TTTCCCEEEEETTEEEEEEECSHH
T ss_pred             cccCCCcceECCCCeeHHHHhHHHHHhcCCcEEEEEECCEEEEEEecCccCCccc-cCccccEEEecCcEEEEeccchHH
Confidence            4899999999999999999999999999999999999999999999999998654 568899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+.++.++..|++.++.+++++.+++.|++++|.|+++.++|||+|++||||||+ .||+||.+||.|++.+++++
T Consensus        89 ~~~l~~~~r~~~~~y~~~~~~~i~v~~la~~l~~~~~~yt~~~~~rP~~v~~lvaG~D~-~gp~Ly~iDp~G~~~~~~~~  167 (264)
T 3h4p_A           89 ARVLIDRARLEAQIYRLTYGEEISIEMLAKKICDIKQAYTQHGGVRPFGVSLLIAGIDK-NEARLFETDPSGALIEYKAT  167 (264)
T ss_dssp             HHHHHTTHHHHHHHHHHTTCSCCCHHHHHHHHHHHHHHTTSBSSCCCCSEEEEEEEEET-TEEEEEEECTTCCCEEESEE
T ss_pred             HHHHHHHHHHHHHhhHHhcCCCCCHHHHHHHHHHHHHHHhhccCCCCeeEEEEEEEEeC-CcCEEEEECCCceEEecCeE
Confidence            99999999999999999999999999999999999999999999999999999999997 58999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhCC
Q 025640          163 AIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGV  242 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~  242 (250)
                      |+|+|+.+++++|++.|+++||++||++++++||..+.++  .++++++|++|++++   ..|++++++||+.++..+.+
T Consensus       168 aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~a~~~--~sg~~iev~vi~~~~---~~~~~l~~~ei~~~~~~~~~  242 (264)
T 3h4p_A          168 AIGSGRPVVMELLEKEYRDDITLDEGLELAITALTKANED--IKPENVDVCIITVKD---AQFKKIPVEEIKKLIEKVKK  242 (264)
T ss_dssp             EESTTHHHHTTTHHHHCCTTCCSHHHHHHHHHHHHHHSSS--CCTTSEEEEEEETTT---TEEEECCTTTTGGGTTTTTT
T ss_pred             EECCCHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhc--cCCCeEEEEEEEeCC---CcEEECCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999986  799999999999875   25999999999999999987


Q ss_pred             CCcccc
Q 025640          243 TQPAAE  248 (250)
Q Consensus       243 ~~~~~~  248 (250)
                      ..++|.
T Consensus       243 ~~~~~~  248 (264)
T 3h4p_A          243 KLNEEN  248 (264)
T ss_dssp             SSSCC-
T ss_pred             hhhcch
Confidence            766553

>1j2p_A Alpha-ring, proteasome alpha subunit; hydrolase; 2.60A {Archaeoglobus fulgidus} SCOP: d.153.1.4 PDB: 1j2q_A*

Probab=100.00  E-value=5.3e-62  Score=414.19  Aligned_cols=235  Identities=41%  Similarity=0.706  Sum_probs=223.4

Q ss_pred             CCCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         1 ~~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      |+++||+++|+|||||||+|||||.+|+.+|+|+|||+++||||||+|+|.+.++.. +++.+||++|+++++|+++|..
T Consensus         4 ~~~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~~-~~~~~KI~~i~~~i~~~~aG~~   82 (246)
T 1j2p_A            4 PQMGYDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLE-KDTIEKIYKIDEHICAATSGLV   82 (246)
T ss_dssp             CCTTSSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSCTTBC-GGGCCSEEECSSSEEEEEEECH
T ss_pred             cccCcCCCCceECCCCeehHHHhHHHHHHcCCcEEEEEECCEEEEEEeccCCccccc-cCccCcEEEECCCEEEEEeEcc
Confidence            445899999999999999999999999999999999999999999999999998766 5688999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce
Q 025640           81 SDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK  160 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~  160 (250)
                      +|++.+.+.++.++..|++.++.+++++.+++.+++.+|.|+++.+.|||++++||||||  +||+||.+||.|++.+++
T Consensus        83 aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rp~~v~~lvaG~D--~gp~Ly~idp~G~~~~~~  160 (246)
T 1j2p_A           83 ADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAGVN--EVPKLYETDPSGALLEYK  160 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEES--SSEEEEEECTTCCEEEBS
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCcccccEEEEEEEEC--CCCEEEEECCCceEEeee
Confidence            999999999999999999999999999999999999999999999999999999999999  589999999999999999


Q ss_pred             EEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEE-eCCCCceeEEECCHHHHHHHHHH
Q 025640          161 AAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVF-LMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       161 ~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~-~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      ++|+|+|+.+++++||+.|+++||++||++++++||..+.++ ..++++++|++|+ +++    .|+.++++||+.++..
T Consensus       161 ~~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~-~~sg~~i~v~vi~~~~~----~~~~l~~~ei~~~~~~  235 (246)
T 1j2p_A          161 ATAIGMGRMAVTEFFEKEYRDDLSFDDAMVLGLVAMGLSIES-ELVPENIEVGYVKVDDR----TFKEVSPEELKPYVER  235 (246)
T ss_dssp             EEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHTS-CCCGGGEEEEEEETTTC----CCEECCHHHHHHHHHH
T ss_pred             EEEECCCcHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhc-cCCCCcEEEEEEEcCCC----ceEECCHHHHHHHHHH
Confidence            999999999999999999999999999999999999999997 8899999999999 643    3899999999999998


Q ss_pred             hCCC
Q 025640          240 HGVT  243 (250)
Q Consensus       240 ~~~~  243 (250)
                      +.+.
T Consensus       236 ~~~~  239 (246)
T 1j2p_A          236 ANER  239 (246)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8543

>1ryp_B 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_B 1g0u_A* 1jd2_A* 1g65_A 1z7q_B 2f16_A* 2fak_A* 2fny_A* 2gpl_A* 2zcy_A* 3bdm_A* 3d29_A* 3dy3_A* 3dy4_A* 3e47_A* 3gpj_A* 3gpt_A* 3gpw_A* 3hye_A* 3mg0_A* ...

Probab=100.00  E-value=1.6e-61  Score=412.21  Aligned_cols=237  Identities=34%  Similarity=0.562  Sum_probs=222.2

Q ss_pred             CCCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         1 ~~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      |+++||+++|+|||||||+|||||.+|+.+|+|+|||+++||||||+|+|.+. .++.+++.+||++|+++++|+++|..
T Consensus         1 ~~~~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~-~l~~~~~~~Ki~~i~~~i~~~~aG~~   79 (250)
T 1ryp_B            1 MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSS-PLAMSETLSKVSLLTPDIGAVYSGMG   79 (250)
T ss_dssp             CCCCCCSBSSCBCTTSCBHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSC-SSBCGGGCCSSEEEETTEEEEEEECH
T ss_pred             CCCcccCCceeECCCCccHHHHhHHHHHHcCCcEEEEEECCEEEEEEeccCCC-ccccCcccCceEEECCCEEEEeeeCH
Confidence            89999999999999999999999999999999999999999999999999985 44556688999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH-HHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecc
Q 025640           81 SDANILINTARVQAQR-YTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW  159 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~~-~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~  159 (250)
                      +|++.+.+.++.++.. |+..++.+++++.+++.++++++.+++..++|||++++||||||+.+||+||.+||.|++.++
T Consensus        80 aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rp~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~  159 (250)
T 1ryp_B           80 PDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPW  159 (250)
T ss_dssp             HHHHHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCCEEEEEEEEETTTEEEEEEECTTSCEEEB
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhcCCcccceEEEEEEEEcCCCCcEEEEECCCCCEEee
Confidence            9999999999999999 999999999999999999999999999889999999999999998668999999999999999


Q ss_pred             eEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCC-----------CceeEEEC
Q 025640          160 KAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPS-----------GKVKYQVC  228 (250)
Q Consensus       160 ~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~-----------~~~~~~~~  228 (250)
                      +++|+|+|+.+++++||+.|+++||++||++++++||..+.++ ..++++++|++|++++.           ....|+++
T Consensus       160 ~~~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~-~~sg~~i~v~vi~~~~~~~~~~~~~~~~~~~~~~~l  238 (250)
T 1ryp_B          160 KATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEG-EFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKL  238 (250)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCCS-CCSTTTEEEEEECSCCGGGTSEESCSSCCCCSEEEC
T ss_pred             ceeEecCccHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhcc-ccCCCCEEEEEEEccccccccccccccCCCCCeEEC
Confidence            9999999999999999999999999999999999999999987 56899999999998731           12359999


Q ss_pred             CHHHHHHHHHH
Q 025640          229 SPEALSKLLVK  239 (250)
Q Consensus       229 ~~~ei~~~~~~  239 (250)
                      +++||+.++..
T Consensus       239 ~~~ei~~~l~~  249 (250)
T 1ryp_B          239 TSQEINDRLEA  249 (250)
T ss_dssp             CHHHHHHHHTT
T ss_pred             CHHHHHHHHHh
Confidence            99999999864

>1iru_B 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_A* 3une_A 3unf_A* 3unh_A

Probab=100.00  E-value=1.2e-61  Score=408.92  Aligned_cols=230  Identities=37%  Similarity=0.632  Sum_probs=219.9

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      .+||+++|+|||||||+|||||.+|+++|+|+|||+++||||||+|+|.+.+ ++.+++.+||++|+++++|+++|..+|
T Consensus         3 ~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~-l~~~~~~~Ki~~i~~~i~~~~aG~~aD   81 (233)
T 1iru_B            3 RGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSI-LYDERSVHKVEPITKHIGLVYSGMGPD   81 (233)
T ss_dssp             CCCCSBSCCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSCEEEEEECCCCCS-SBCSTTCCSSEESSSSEEEEEEECHHH
T ss_pred             CCccCCceeECCCCeEehhHhHHHHHHcCCcEEEEEeCCEEEEEEEecCCcc-ccccccCCeEEEECCCEEEEEEEccHH
Confidence            5899999999999999999999999999999999999999999999999865 444568899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+.++.++..|++.++.+++++.+++.+++.+|.|+++.++|||++++||||||+ .||+||.+||.|++.+++++
T Consensus        82 ~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~y~~~~~~rP~~v~~lvaG~D~-~gp~Ly~id~~G~~~~~~~~  160 (233)
T 1iru_B           82 YRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWNE-GRPYLFQSDPSGAYFAWKAT  160 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSEEEEEEEECS-SSEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCcCCCCCcEEEEEEEEEeC-CCCeEEEECCCCCEEEeeEE
Confidence            99999999999999999999999999999999999999999989999999999999996 58999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 025640          163 AIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH  240 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~  240 (250)
                      ++|+|+.+++++||+.|+++||++||++++++||..+.+++ .++++++|++|++++     ++.++++||+.++..+
T Consensus       161 aiG~gs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~d-~sg~~i~v~vi~~~g-----~~~l~~~ei~~~~~~~  232 (233)
T 1iru_B          161 AMGKNYVNGKTFLEKRYNEDLELEDAIHTAILTLKESFEGQ-MTEDNIEVGICNEAG-----FRRLTPTEVKDYLAAI  232 (233)
T ss_dssp             EESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHTTCCSC-CCSSSEEEEEEETTE-----EEECCHHHHHHHHTTC
T ss_pred             EECCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcc-CCCCCEEEEEEECCC-----EEECCHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999988 779999999999986     8999999999998754

>1ryp_E 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_D* 1g65_D 2f16_D* 2fak_D* 2fny_D* 2gpl_D* 3d29_D* 3dy3_D* 3dy4_D* 3e47_D* 3gpj_D* 3gpt_D* 3gpw_D* 3hye_D* 3mg0_D* 3mg4_D* 3okj_D* 3shj_D* 3tdd_D* 2z5c_C ...

Probab=100.00  E-value=1.2e-61  Score=411.24  Aligned_cols=233  Identities=38%  Similarity=0.623  Sum_probs=223.2

Q ss_pred             CCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHH
Q 025640            6 DSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANI   85 (250)
Q Consensus         6 d~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~   85 (250)
                      |+++|+|||||||||||||.+|+.+|+|+|||+++||||||+|+|.++|+++ +++.+||++|+++++|+++|..+|++.
T Consensus         1 d~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~-~~~~~Ki~~i~~~i~~~~aG~~aD~~~   79 (242)
T 1ryp_E            1 DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEKIVEIDRHIGCAMSGLTADARS   79 (242)
T ss_dssp             CCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEECSSCEEEEEECCCSSTTBC-GGGCCCEEEEETTEEEEEEESGGGHHH
T ss_pred             CCCCceECCCCcChHHHhHHHHHHcCCCEEEEEECCEEEEEEeecCCCcCcc-CccCCceEEEcCCEEEEEeecHHHHHH
Confidence            7899999999999999999999999999999999999999999999999988 668899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCC------CcceeEEEEEEEEeCCCCeEEEEECCCCceecc
Q 025640           86 LINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGG------LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW  159 (250)
Q Consensus        86 l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~------~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~  159 (250)
                      +.+.++.++..|++.++.+++++.+++.+++++|.|+++.+      .|||++++||||||+.+||+||.+||.|++.++
T Consensus        80 l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~~~~l~~RP~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~  159 (242)
T 1ryp_E           80 MIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRY  159 (242)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCBSSCCSEEEEEEEEETTTEEEEEEECTTSCEEEB
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcccccccCcceEEEEEEEEeCCCCCEEEEECCCCCEecc
Confidence            99999999999999999999999999999999999999888      999999999999996568999999999999999


Q ss_pred             eEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          160 KAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       160 ~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      +++|+|+|+.+++++||+.|+++||++||++++++||..+.++ ..++++++|++|++++    .+++++++||+.++..
T Consensus       160 ~~~aiGsgs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~-~~sg~~i~v~vi~~~~----~~~~~~~~ei~~~~~~  234 (242)
T 1ryp_E          160 NAKAIGSGSEGAQAELLNEWHSSLTLKEAELLVLKILKQVMEE-KLDENNAQLSCITKQD----GFKIYDNEKTAELIKE  234 (242)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSS-CCCTTSEEEEEEETTT----EEEECCHHHHHHHHHH
T ss_pred             CEEEECCCCHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHhhc-cCCCCcEEEEEEECCC----CeEECCHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999998 7889999999999987    3899999999999998


Q ss_pred             hCCCC
Q 025640          240 HGVTQ  244 (250)
Q Consensus       240 ~~~~~  244 (250)
                      +.+.+
T Consensus       235 ~~~~~  239 (242)
T 1ryp_E          235 LKEKE  239 (242)
T ss_dssp             HHHHH
T ss_pred             Hhhhh
Confidence            85433

>3nzj_F Proteasome component C1; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 1z7q_G* 3nzw_F* 3nzx_F* 3un4_F* 3un8_F* 4b4t_G 4g4s_G* 3bdm_F* 1fnt_G* 2zcy_F*

Probab=100.00  E-value=1.8e-60  Score=411.74  Aligned_cols=235  Identities=34%  Similarity=0.561  Sum_probs=220.5

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      .+||+++|+|||||||||||||.+|+++|+|+|||+++||||||+|+|.++|+++.+ ..+||++|++||+|+++|+.+|
T Consensus         6 ~~yd~~~t~fSP~Grl~QvEYA~kAv~~GtT~Vgik~kdGVVlAaD~r~t~gl~~~~-~~~KI~~I~d~i~~~~aG~~aD   84 (288)
T 3nzj_F            6 TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQ-KNVKIQVVDRHIGCVYSGLIPD   84 (288)
T ss_dssp             CCTTSSTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEEEEECCTTBCTT-CSCCCEEETTTEEEEEEECHHH
T ss_pred             CCccCCcccCCCCCchHHHHHHHHHHhcCCcEEEEEECCEEEEEEcCCcccCCcccc-ccceEEEEcCCEEEEecCcHHH
Confidence            489999999999999999999999999999999999999999999999999999876 6799999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+.++.++..|++.++.+++++.+++.|++++|.|++++++|||+|++||||||+ .||+||++||.|++.+++++
T Consensus        85 ~~~l~~~lr~e~~~y~~~~~~~i~v~~lA~~l~~~l~~yt~~~~~rP~gv~~lvaG~D~-~Gp~Ly~iDp~G~~~~~~~~  163 (288)
T 3nzj_F           85 GRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDK-NGAHLYMLEPSGSYWGYKGA  163 (288)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEET-TEEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHHHHHHHHHHHhccCCCceEEEEEEEEeC-CCCEEEEECCCCCEEEcCEE
Confidence            99999999999999999999999999999999999999999999999999999999998 58999999999999999999


Q ss_pred             EEeCChHHHHHHHHhh---CCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEe-CCCCceeEEECCHHHHHHHHH
Q 025640          163 AIGANNQAAQSILKQD---YKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFL-MPSGKVKYQVCSPEALSKLLV  238 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~---~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~-~~~~~~~~~~~~~~ei~~~~~  238 (250)
                      |+|+++++++++||+.   |+++||++||++++++||..+.+++..+++.++|++|++ +..+  .++.++.++++.--.
T Consensus       164 aiGsgs~~a~~~Lek~~~~~~~~ms~eEAv~la~~al~~a~~~~~~~~~~iev~vIt~~~~~~--~~~~vp~~~~~~~~~  241 (288)
T 3nzj_F          164 ATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNG--LHKFVKGDLLQEAID  241 (288)
T ss_dssp             EESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSEEEEEEEEEETTTSTT--CCEECCHHHHHHHHH
T ss_pred             EEcCcHHHHHHHHHHhccccCCCCCHHHHHHHHHHHHHHHHhcccCCCCeEEEEEEEecCCCc--eEEECCHHHHHHHHH
Confidence            9999999999999999   999999999999999999999999888999999999998 4423  357788877766544


Q ss_pred             HhC
Q 025640          239 KHG  241 (250)
Q Consensus       239 ~~~  241 (250)
                      ..+
T Consensus       242 ~~~  244 (288)
T 3nzj_F          242 FAQ  244 (288)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>1iru_F 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_E* 3une_E 3unf_E* 3unh_E

Probab=100.00  E-value=9.3e-61  Score=409.97  Aligned_cols=233  Identities=32%  Similarity=0.544  Sum_probs=221.2

Q ss_pred             CCC-CCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCc
Q 025640            1 MSR-RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGI   79 (250)
Q Consensus         1 ~~~-~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~   79 (250)
                      |.| +||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|+|.++++.   ++.+||++|+++++|+++|.
T Consensus         1 m~~~~yd~~~t~fsP~Grl~QvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r~~~gl~---~~~~KI~~i~~~i~~~~aG~   77 (263)
T 1iru_F            1 MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELA---AHQKKILHVDNHIGISIAGL   77 (263)
T ss_dssp             ---CTTTSCTTCCCTTSCCHHHHHHHHHHHHSCCEEEEECSSEEEEEEECCCSSTTB---CCCCCEEEEETTEEEEEEEC
T ss_pred             CCcCCCCCCCccCCCCCeehHHHHHHHHHHcCCcEEEEEeCCEEEEEEecccccccc---cchhcEEEEcCCEEEEEeCC
Confidence            666 89999999999999999999999999999999999999999999999999974   36799999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecc
Q 025640           80 MSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW  159 (250)
Q Consensus        80 ~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~  159 (250)
                      .+|++.+.+.++.++..|++.++.+++++.+++.+++.+|.|+++.+.|||+|++||||||+ .||+||.+||+|++.++
T Consensus        78 ~aD~~~l~~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~~~t~~~~~RP~~v~~lvaG~D~-~gp~Ly~idp~G~~~~~  156 (263)
T 1iru_F           78 TADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDD-MGPHIFQTCPSANYFDC  156 (263)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEET-TEEEEEEECSSSCEEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHhhcccccccceEEEEEEEEcC-CCCEEEEECCCCCEEEe
Confidence            99999999999999999999999999999999999999999999989999999999999998 58999999999999999


Q ss_pred             eEEEEeCChHHHHHHHHhhCCC--CCCHHHHHHHHHHHHHHhhcCC-CCCCCcEEEEEEEeCCCCceeEEECCHHHHHHH
Q 025640          160 KAAAIGANNQAAQSILKQDYKD--DISREEAVQLALKVLSKTMDST-SLTSDKLELAEVFLMPSGKVKYQVCSPEALSKL  236 (250)
Q Consensus       160 ~~~a~G~g~~~~~~~L~~~~~~--~~s~~ea~~l~~~~l~~~~~~~-~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~  236 (250)
                      +++|+|+|+.+++++||+.|++  +||++||++++++||..+.+++ ..++++++|++|++++    .|++++++||+.+
T Consensus       157 ~~~aiGsgs~~a~~~Le~~~~~~~~ms~eea~~la~~al~~~~~rd~~~sg~~iev~vi~~~~----~~~~l~~~ei~~~  232 (263)
T 1iru_F          157 RAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDL----EFTIYDDDDVSPF  232 (263)
T ss_dssp             SEEEESTTHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCTTCCCCTTTEEEEEEETTE----EEEEECSGGGHHH
T ss_pred             eEEEcCcccHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHhccccCCCCcEEEEEEECCC----CeEECCHHHHHHH
Confidence            9999999999999999999998  9999999999999999999998 4889999999999884    3899999999999


Q ss_pred             HHHhC
Q 025640          237 LVKHG  241 (250)
Q Consensus       237 ~~~~~  241 (250)
                      +..+.
T Consensus       233 ~~~~~  237 (263)
T 1iru_F          233 LEGLE  237 (263)
T ss_dssp             HTTCC
T ss_pred             HHHHh
Confidence            98875

>1ryp_G 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_F* 1g65_F 1vsy_G 2f16_F* 2fak_F* 2fny_F* 2gpl_F* 3d29_F* 3dy3_F* 3dy4_F* 3e47_F* 3gpj_F* 3gpt_F* 3gpw_F* 3hye_F* 3l5q_L 3mg0_F* 3mg4_F* 3okj_F* 3shj_F* ...

Probab=100.00  E-value=1.1e-59  Score=399.28  Aligned_cols=231  Identities=35%  Similarity=0.561  Sum_probs=217.5

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      ++||+++|+|||||||+|||||.+|+.+|+|+|||+++||||||+|+|.++|+++.++ .+||++|+++++|+++|..+|
T Consensus         2 ~~yd~~~t~fsp~Grl~QvEya~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~-~~KI~~i~~~i~~~~aG~~aD   80 (244)
T 1ryp_G            2 TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQK-NVKIQVVDRHIGCVYSGLIPD   80 (244)
T ss_dssp             CCTTSSTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEEEECCCTTBCTTT-SCCCEEETTTEEEEEEECHHH
T ss_pred             CCccCCcccCCcCCchHHHHhHHHHHHCCCCEEEEEECCEEEEEEecccCCCCccccc-cCceEEecCCEEEEEcccHHH
Confidence            5899999999999999999999999999999999999999999999999999998875 499999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+.++.++..|++.++.+++++.+++.+++.+|.|+++++.|||++++||||||+ .||+||.+||+|++.+++++
T Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v~~lvaG~D~-~gp~Ly~idp~G~~~~~~~~  159 (244)
T 1ryp_G           81 GRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDK-NGAHLYMLEPSGSYWGYKGA  159 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEET-TEEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCccCceEEEEEEEEeC-CcCEEEEECCCCCEEEeeEE
Confidence            99999999999999999999999999999999999999999988999999999999997 58999999999999999999


Q ss_pred             EEeCChHHHHHHHHhh---CCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEe---CCCCceeEEECCHHHHHHH
Q 025640          163 AIGANNQAAQSILKQD---YKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFL---MPSGKVKYQVCSPEALSKL  236 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~---~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~---~~~~~~~~~~~~~~ei~~~  236 (250)
                      |+|+|+.+++++||+.   |+++||++||++++++||..+.+++..++++++|++|++   +|     ++.+.++++-..
T Consensus       160 aiG~gs~~a~~~Le~~~~~~~~~ms~eea~~la~~al~~~~~~d~~s~~~iev~vi~~~~~~g-----~~~~~~~~~~~~  234 (244)
T 1ryp_G          160 ATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNG-----LHKFVKGDLLQE  234 (244)
T ss_dssp             EESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSCEEEEEEEEETTTTTT-----SEEECCTHHHHH
T ss_pred             EECCChHHHHHHHHHhHhhcCCCCCHHHHHHHHHHHHHHHHhccCCCCCeEEEEEEEecCCCC-----eeeeChHHHHHH
Confidence            9999999999999997   999999999999999999999999999999999999997   44     567666676555


Q ss_pred             HHHh
Q 025640          237 LVKH  240 (250)
Q Consensus       237 ~~~~  240 (250)
                      ..+.
T Consensus       235 ~~~~  238 (244)
T 1ryp_G          235 AIDF  238 (244)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>1ryp_F 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_E* 1g65_E 2f16_E* 2fak_E* 2fny_E* 2gpl_E* 3d29_E* 3dy3_E* 3dy4_E* 3e47_E* 3gpj_E* 3gpt_E* 3gpw_E* 3hye_E* 3mg0_E* 3mg4_E* 3oeu_E* 3oev_E* 3okj_E* 3shj_E* ...

Probab=100.00  E-value=2e-60  Score=401.44  Aligned_cols=225  Identities=35%  Similarity=0.541  Sum_probs=214.8

Q ss_pred             CCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHH
Q 025640            4 RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDA   83 (250)
Q Consensus         4 ~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~   83 (250)
                      +||+++|+|||||||+|||||++|+++|+|+|||+++||||||+|+|.+.++.   ++.+||++|+++++|+++|..+|+
T Consensus         4 ~yd~~~t~fsp~Grl~QvEyA~~av~~Gtt~vgi~~~dgVvlaaD~r~~~~l~---~~~~Ki~~i~~~i~~~~aG~~aD~   80 (233)
T 1ryp_F            4 NYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELS---SYQKKIIKCDEHMGLSLAGLAPDA   80 (233)
T ss_dssp             HHSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSEEEEEEECCCSSTTB---CCCCCEEEEETTEEEEEEECHHHH
T ss_pred             cccCCCccCCCCCeehHHHHHHHHHHcCCCEEEEEcCCEEEEEEEeccccccc---cccCcEEEEcCCEEEEEEechHHH
Confidence            79999999999999999999999999999999999999999999999999975   367999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEE
Q 025640           84 NILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAA  163 (250)
Q Consensus        84 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a  163 (250)
                      +.+.+.++.++..|++.++.+++++.+++.+++.+|.|+|+.+.|||++++||||||+ .||+||.+||+|++.+++++|
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rp~~v~~lvaG~D~-~gp~Ly~idp~G~~~~~~~~a  159 (233)
T 1ryp_F           81 RVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDK-SGAHLLEFQPSGNVTELYGTA  159 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEET-TEEEEEEECTTSCEEEESEEE
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCCcCcceEEEEEEEeC-CcCEEEEECCCCCeeeeeEEE
Confidence            9999999999999999999999999999999999999999999999999999999998 589999999999999999999


Q ss_pred             EeCChHHHHHHHHhhCCC--CC--CHHHHHHHHHHHHHHhhcCC-CCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 025640          164 IGANNQAAQSILKQDYKD--DI--SREEAVQLALKVLSKTMDST-SLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL  237 (250)
Q Consensus       164 ~G~g~~~~~~~L~~~~~~--~~--s~~ea~~l~~~~l~~~~~~~-~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~  237 (250)
                      +|+|+.+++++||+.|++  +|  |++||+++++++|..+. ++ ..++++++|++|++++    .|++++++||+.++
T Consensus       160 iG~gs~~a~~~Le~~~~~~~~m~~s~eea~~~a~~al~~~~-~d~~~s~~~i~v~vi~~~~----~~~~l~~~ei~~~l  233 (233)
T 1ryp_F          160 IGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSL-RDESLTVDNLSIAIVGKDT----PFTIYDGEAVAKYI  233 (233)
T ss_dssp             ESTTHHHHHHHHHHHHHHHTTCCSCHHHHHHHHHHHHTTSC-CSSCCCTTTEEEEEEETTE----EEEEEEGGGGGGGC
T ss_pred             ECCCcHHHHHHHHHHhccccccCCCHHHHHHHHHHHHHHHh-hcccCCCCcEEEEEEECCC----CEEECCHHHHHhhC
Confidence            999999999999999998  99  99999999999999999 67 5789999999999885    38999999997653

>1q5q_A Proteasome alpha-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, RH erythropolis, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4 PDB: 2h6j_A 1q5r_A

Probab=100.00  E-value=4.2e-51  Score=349.26  Aligned_cols=225  Identities=20%  Similarity=0.255  Sum_probs=196.7

Q ss_pred             ccccCCCCccc-ccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHH
Q 025640            9 TTIFSPEGRLY-QVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILI   87 (250)
Q Consensus         9 ~~~f~p~G~l~-qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~   87 (250)
                      +..|||||++. |||||.+|+.+|+|+|||+++||||||+|+|        +++.+||++|++||+|+++|..+|++.+.
T Consensus         4 p~~~sPe~~~~~qvEYA~~av~~Gtt~vgi~~~dgVVlaaD~r--------s~~~~KI~~I~d~i~~~~aG~~aD~~~l~   75 (259)
T 1q5q_A            4 PYYASAEQIMRDRSELARKGIARGRSVVVLTFRDGVLFVAENP--------STALHKVSELYDRLGFAAVGKYNEFENLR   75 (259)
T ss_dssp             -----CHHHHHHHHHHHHHHHHTSCCEEEEECSSEEEEEECCS--------CSSSCSEEEEETTEEEEEEECHHHHHHHH
T ss_pred             CcccCHHHHHHHHHHHHHHHHhcCCcEEEEEeCCEEEEEEecC--------CCCcCcEEEeCCCEEEEEccCHHHHHHHH
Confidence            45689999995 9999999999999999999999999999998        35789999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhCC-CCCHHHHHHHHHH-HHhhccccCCCcceeEEEEEEEEe--C-CCCeEEEEECCCCcee-cceE
Q 025640           88 NTARVQAQRYTYAYQE-PMPVEQLVQSLCD-TKQGYTQFGGLRPFGVSFLFAGWD--K-NYGFQLYMSDPSGNYG-GWKA  161 (250)
Q Consensus        88 ~~~~~~~~~~~~~~~~-~~~~~~la~~l~~-~~~~~~~~~~~rP~~~~~iv~G~d--~-~~~~~Ly~vd~~G~~~-~~~~  161 (250)
                      +.++.++..+.+.++. +++++.+++.+++ +.|.|+.  +.|||+|++||||||  + ..||+||++||+|++. .+++
T Consensus        76 ~~~~~~~~~~~~~~~~~~i~v~~la~~l~~~l~q~yt~--~~rP~~v~~lvaG~D~~~~~~gp~Ly~idp~G~~~~~~~~  153 (259)
T 1q5q_A           76 RAGIVHADMRGYSYDRRDVTGRSLANAYAQTLGTIFTE--QPKPYEVEICVAEVGRVGSPKAPQLYRITYDGSIVDEQHF  153 (259)
T ss_dssp             HHHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHHHHHH--SSSCCCEEEEEEECCCSSCCCCCEEEEEETTSCEEEESSE
T ss_pred             HHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHhcc--CCCCceEEEEEEEEcccCCCCCCEEEEECCCCceeeCCCE
Confidence            9999999999999884 9999999999999 6566663  689999999999999  3 4689999999999999 8899


Q ss_pred             EEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhh-----cCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHH
Q 025640          162 AAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTM-----DSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKL  236 (250)
Q Consensus       162 ~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~-----~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~  236 (250)
                      +++|++++.++++||+.|+++|+++||++++++||..+.     +++. ++++++|++|++++.+ ..|++++++||+.+
T Consensus       154 ~aiG~gs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~~~~~rd~-sg~~iev~vi~~~~~~-~~~~~l~~~ei~~~  231 (259)
T 1q5q_A          154 VVMGGTTEPIATAMRESYRADLDLEAAVGIAVNALRQGGAGEGEKRNV-DVASLEVAVLDQSRPR-RAFRRIAGTALEQL  231 (259)
T ss_dssp             EEESSSHHHHHHHHHHHCCTTCCHHHHHHHHHHHHTTCC--------C-CSSCSEEEEEETTSSS-CCEEECCHHHHHTT
T ss_pred             EEECCChHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHhhcccccccC-CCCcEEEEEEECCCCc-CCeEECCHHHHHHH
Confidence            999999999999999999999999999999999999998     7887 9999999999998422 24999999999999


Q ss_pred             HHHhCCCCc
Q 025640          237 LVKHGVTQP  245 (250)
Q Consensus       237 ~~~~~~~~~  245 (250)
                      +..+.+.+.
T Consensus       232 ~~~~~~~~~  240 (259)
T 1q5q_A          232 VPAEPAAAS  240 (259)
T ss_dssp             SCCC-----
T ss_pred             HHHhhhccc
Confidence            987765443

>3mi0_A Proteasome subunit alpha; enzyme inhibitors, lactones, proteasome endopeptidase comple mycobacterium tuberculosis, hydrolase; HET: SA6; 2.20A {Mycobacterium tuberculosis} SCOP: d.153.1.4 PDB: 3h6f_A 3krd_A* 3h6i_A* 3mka_A 2fhh_A* 2fhg_A 3hfa_D 3hf9_A 3mfe_D

Probab=100.00  E-value=1.3e-49  Score=337.33  Aligned_cols=233  Identities=23%  Similarity=0.278  Sum_probs=192.4

Q ss_pred             CCCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         1 ~~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      |+--|+.++..|..+    ++|||.||+++|+|+|||+++||||||+|+|        +++.+||++|++||+|+++|..
T Consensus         1 ~~~~~~~~p~~~~~~----r~EYA~~av~~GtT~vgi~~kdgVVlaadkr--------~~~~~KI~~I~d~i~~~~aG~~   68 (248)
T 3mi0_A            1 MSFPYFISPEQAMRE----RSELARKGIARAKSVVALAYAGGVLFVAENP--------SRSLQKISELYDRVGFAAAGKF   68 (248)
T ss_dssp             -------CHHHHHHH----HHHHHHHHHHTSCCEEEEEETTEEEEEEECC--------CSSSCSEEEEETTEEEEEEECH
T ss_pred             CCCCccCCHHHhccc----chHHHHHHHhCCCcEEEEEeCCEEEEEEeCC--------CCCCCCeEEECCCEEEEEccCH
Confidence            444455444444433    4899999999999999999999999999999        3478999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHH-HHHhhccccCCCcceeEEEEEEEEeC---CCCeEEEEECCCCc
Q 025640           81 SDANILINTARVQAQRYTYAYQ-EPMPVEQLVQSLC-DTKQGYTQFGGLRPFGVSFLFAGWDK---NYGFQLYMSDPSGN  155 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~~~~~~~~-~~~~~~~la~~l~-~~~~~~~~~~~~rP~~~~~iv~G~d~---~~~~~Ly~vd~~G~  155 (250)
                      +|++.|.+.++.++..|++.++ .+++++.|++.++ .+.|.|++  +.|||+|++||||||+   .+||+||++||+|+
T Consensus        69 aD~~~l~~~~~~~~~l~~~~~~~~~i~v~~la~~l~~~l~q~yt~--~~rP~gv~~liaG~D~~~~~~gp~Ly~~Dp~G~  146 (248)
T 3mi0_A           69 NEFDNLRRGGIQFADTRGYAYDRRDVTGRQLANVYAQTLGTIFTE--QAKPYEVELCVAEVAHYGETKRPELYRITYDGS  146 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHHHHHHHHHHH--SSSCCCEEEEEEECCCTTCCCCCEEEEECTTSC
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHhcc--CCCCceEEEEEEEEcCCCCCCCCEEEEECCCeE
Confidence            9999999999999999999999 8999999999999 67788887  7899999999999997   36899999999999


Q ss_pred             eec-ceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhc------CCCCCCCcEEEEEEEeCCCCceeEEEC
Q 025640          156 YGG-WKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMD------STSLTSDKLELAEVFLMPSGKVKYQVC  228 (250)
Q Consensus       156 ~~~-~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~------~~~~~~~~iei~ii~~~~~~~~~~~~~  228 (250)
                      +.. ++++|+|+|+++++++||++|+++|+++||++++++||..+.+      +...++.+++|++|++++. ...|+++
T Consensus       147 ~~~e~~~~a~Gsgs~~a~~~Le~~y~~~mt~eeai~la~~aL~~~~~~~~~~~~~~~~~~~iev~vv~~~g~-~~~f~~l  225 (248)
T 3mi0_A          147 IADEPHFVVMGGTTEPIANALKESYAENASLTDALRIAVAALRAGSADTSGGDQPTLGVASLEVAVLDANRP-RRAFRRI  225 (248)
T ss_dssp             EEEESSEEEESSCHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHC------------CCTTEEEEEEETTSS-SCCEEEC
T ss_pred             EeecccEEEECccHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhcccCcccccCCCcEEEEEEECCCC-cccEEEC
Confidence            994 9999999999999999999999999999999999999999982      2367889999999999862 2469999


Q ss_pred             CHHHHHHHHHHhCCCCcccc
Q 025640          229 SPEALSKLLVKHGVTQPAAE  248 (250)
Q Consensus       229 ~~~ei~~~~~~~~~~~~~~~  248 (250)
                      +++||+.++..+..++.+.+
T Consensus       226 ~~~ei~~~l~~~~~~~~~~~  245 (248)
T 3mi0_A          226 TGSALQALLVDQESPQSDGE  245 (248)
T ss_dssp             CHHHHHHTC-----------
T ss_pred             CHHHHHHHHHHcCCCccccc
Confidence            99999999999987776544

>3h4p_a Proteasome subunit beta; core particle, cytoplasm, hydrolase, protease, threonine protease; 4.10A {Methanocaldococcus jannaschii}

Probab=100.00  E-value=1.2e-48  Score=326.45  Aligned_cols=210  Identities=24%  Similarity=0.392  Sum_probs=194.2

Q ss_pred             CccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 025640           31 AGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQL  110 (250)
Q Consensus        31 g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l  110 (250)
                      |+|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++.+++++.+
T Consensus         1 Gtt~vgi~~~dgVvlaaD~r~~~g~~i~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~l   80 (219)
T 3h4p_a            1 MTTTVGLICDDAVILATDKRASLGNLVADKEAKKLYKIDDYIAMTIAGSVGDAQAIVRLLIAEAKLYKMRTGRNIPPLAC   80 (219)
T ss_dssp             -CCEEEEEETTEEEEECCCCEEETTEEEETTCCCEEEEETTEEEECCSCHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHH
T ss_pred             CccEEEEEECCEEEEEEcCCcccCCEeeccccceeEEecCCEEEEeeEcHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            78999999999999999999999988777899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce-EEEEeCChHHHHHHHHhhCCCCCCHHHHH
Q 025640          111 VQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK-AAAIGANNQAAQSILKQDYKDDISREEAV  189 (250)
Q Consensus       111 a~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~-~~a~G~g~~~~~~~L~~~~~~~~s~~ea~  189 (250)
                      ++.+++.+|.+    +.|||++++||||||+..||+||.+||+|++.+++ ++|+|+|+++++++||+.|+++|+++||+
T Consensus        81 a~~l~~~~~~~----~~~P~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~~~~ms~eea~  156 (219)
T 3h4p_a           81 ATLLSNILHSS----RMFPFLTQIIIGGYDLLEGAKLFSLDPLGGMNEEKTFTATGSGSPIAYGVLEAGYDRDMSVEEGI  156 (219)
T ss_dssp             HHHHHHHHHHT----TTTTCCCCCEEEEEETTTEEEEEEECSSCCEEECSSEEEESTTHHHHHHHHHTSCCTTCCHHHHH
T ss_pred             HHHHHHHHHHh----cCCCceEEEEEEEEeCCCCcEEEEECCCCceEecCCEEEEcCCHHHHHHHHHHhcCCCCCHHHHH
Confidence            99999999876    36899999999999986689999999999999999 99999999999999999999999999999


Q ss_pred             HHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhCCCCccccC
Q 025640          190 QLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQPAAET  249 (250)
Q Consensus       190 ~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~~  249 (250)
                      +++++||..+.+++..++++++|++|++++     |++++++||+.++.++.+....+++
T Consensus       157 ~la~~al~~~~~rd~~sg~~i~v~vi~~~g-----~~~l~~~ei~~~l~~~~~~~~~~~~  211 (219)
T 3h4p_a          157 KLALNALKSAMERDTFSGNGISLAVITKDG-----VKIFEDEEIEKILDSMKAKPKKKTT  211 (219)
T ss_dssp             HHHHHHHHHHHTSCSSCCSCCCEEEEETTE-----EEECCHHHHHHHHHHCC--------
T ss_pred             HHHHHHHHHHHhhcCCCCCcEEEEEEeCCC-----eEEcCHHHHHHHHHHhhcccccccc
Confidence            999999999999999999999999999986     9999999999999999987777665

>1yar_H Proteasome beta subunit; proteasome 20S, PA26 proteasome activator 11S, hydrolase-HYD activator complex; 1.90A {Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_H 1yau_H 3ipm_H 1pma_B 3jrm_H 3c92_H 3c91_H 3jse_H 3jtl_H

Probab=100.00  E-value=5e-47  Score=316.33  Aligned_cols=207  Identities=20%  Similarity=0.363  Sum_probs=191.6

Q ss_pred             HHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCC
Q 025640           26 EAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPM  105 (250)
Q Consensus        26 ~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~  105 (250)
                      +++.+|+|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.+++++
T Consensus         3 ~~~~~Gtt~vgi~~~dgVvlaaD~r~~~g~l~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~   82 (217)
T 1yar_H            3 QTLETGTTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNM   82 (217)
T ss_dssp             ------CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCccEEEEEeCCEEEEEEcCCCCCCCEEecCccCCeEEeCCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence            57889999999999999999999999998777777899999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCH
Q 025640          106 PVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISR  185 (250)
Q Consensus       106 ~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~  185 (250)
                      +++.+++.+++.+|.+    +.|||++++||||||  .||+||.+||+|++.+++++|+|+|+.+++++||+.|+++||+
T Consensus        83 ~v~~la~~l~~~~~~~----r~rp~~v~~lvaG~D--~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~s~  156 (217)
T 1yar_H           83 PIEAVATLLSNMLNQV----KYMPYMVQLLVGGID--TAPHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTV  156 (217)
T ss_dssp             CHHHHHHHHHHHHHHT----TTSCCCEEEEEEEES--SSEEEEEECTTCCEEEESEEEESTTHHHHHHHHHHHCCTTCCH
T ss_pred             CHHHHHHHHHHHHHhc----CCCCceEEEEEEEEC--CCCEEEEECCCCCeEecCEEEEcCCHHHHHHHHHhhcccCCCH
Confidence            9999999999999875    378999999999999  4899999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEe-CCCCceeEEECCHHHHHHHHHHhCCC
Q 025640          186 EEAVQLALKVLSKTMDSTSLTSDKLELAEVFL-MPSGKVKYQVCSPEALSKLLVKHGVT  243 (250)
Q Consensus       186 ~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~-~~~~~~~~~~~~~~ei~~~~~~~~~~  243 (250)
                      +||++++++||..+.+++..++++++|++|++ ++     ++.++++||+.++..+...
T Consensus       157 eea~~la~~al~~~~~rd~~s~~~i~v~vi~~~~g-----~~~~~~~ei~~~~~~~~~~  210 (217)
T 1yar_H          157 DEGVDLVIRAISAAKQRDSASGGMIDVAVITRKDG-----YVQLPTDQIESRIRKLGLI  210 (217)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTCCSCCEEEEEETTTE-----EEECCHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHhccCCCCCcEEEEEEECCCC-----EEEcCHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999998 54     8999999999999988754

>1j2q_H Proteasome beta subunit; ubiquitin, CP, hydrolase; HET: CIB; 2.83A {Archaeoglobus fulgidus} SCOP: d.153.1.4

Probab=100.00  E-value=1.8e-46  Score=309.77  Aligned_cols=201  Identities=26%  Similarity=0.430  Sum_probs=191.3

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|.++.+++.+||++|++|++|+++|..+|++.+.+.++.++..|++.++.+++++.++
T Consensus         1 tt~vgi~~~dgVvlaad~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (202)
T 1j2q_H            1 TTTVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRERKPTVRAIA   80 (202)
T ss_dssp             CCEEEEEETTEEEEEEECCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CcEEEEEeCCEEEEEECCCcCcCCEEeeccccCEEEcCCCEEEEecccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            58999999999999999999998777777899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce-EEEEeCChHHHHHHHHhhCCCCCCHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK-AAAIGANNQAAQSILKQDYKDDISREEAVQ  190 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~-~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~  190 (250)
                      +.+++.+|.+    +.|||++++||||||+ .||+||.+||+|++.+++ ++|+|+|+++++++||+.|+++||++||++
T Consensus        81 ~~l~~~~~~~----r~rp~~~~~lvaG~D~-~gp~Ly~id~~G~~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s~eea~~  155 (202)
T 1j2q_H           81 TLTSNLLNSY----RYFPYLVQLLIGGIDS-EGKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVE  155 (202)
T ss_dssp             HHHHHHHHHT----TTSCCCEEEEEEEEET-TEEEEEEECTTCCEEEESSEEEESTTHHHHHHHHHHHCCTTCCHHHHHH
T ss_pred             HHHHHHHHhh----CCCCceEEEEEEEEeC-CCCEEEEECCCCCeeecCCEEEEcCCHHHHHHHHHhhcCCCcCHHHHHH
Confidence            9999999875    3789999999999998 589999999999999999 999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhCC
Q 025640          191 LALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGV  242 (250)
Q Consensus       191 l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~  242 (250)
                      ++++||..+.+++..++++++|++|++++     ++.++++||+.++.++++
T Consensus       156 la~~al~~~~~~d~~s~~~i~v~vi~~~g-----~~~l~~~ei~~~~~~~~~  202 (202)
T 1j2q_H          156 LAVRAIYSAMKRDSASGDGIDVVKITEDE-----FYQYSPEEVEQILAKFRK  202 (202)
T ss_dssp             HHHHHHHHHHTTCTTSCSCEEEEEECSSC-----EEECHHHHHHHHGGGTTC
T ss_pred             HHHHHHHHHHhcCCCCCCcEEEEEEeCCC-----eEEeCHHHHHHHHHHhhC
Confidence            99999999999999999999999999986     899999999999987753

>1q5r_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, hydrolase; 3.10A {Rhodococcus erythropolis} SCOP: d.153.1.4 PDB: 2h6j_H

Probab=100.00  E-value=1.1e-46  Score=326.45  Aligned_cols=218  Identities=21%  Similarity=0.231  Sum_probs=200.0

Q ss_pred             HHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCC
Q 025640           24 AMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQE  103 (250)
Q Consensus        24 a~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~  103 (250)
                      |.+|+.+|+|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++.
T Consensus        58 a~~Av~~GtTiVgIk~kdGVVlAaD~r~t~G~li~~~~~~KI~~I~~~i~~~~aG~~aD~~~l~~~~r~~~~~y~~~~g~  137 (294)
T 1q5r_H           58 SGDLAPHGTTIVALTYKGGVLLAGDRRATQGNLIASRDVEAVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGV  137 (294)
T ss_dssp             --CCSCBCCCEEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHhcCceEEEEEECCEEEEEEcCccccCceeecCCcceEEEECCcEEEEEeecHHHHHHHHHHHHHHHHHhhHhhCC
Confidence            88999999999999999999999999999987777788999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCC-----eEEEEECCCCceecc--eEEEEeCChHHHHHHHH
Q 025640          104 PMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYG-----FQLYMSDPSGNYGGW--KAAAIGANNQAAQSILK  176 (250)
Q Consensus       104 ~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~-----~~Ly~vd~~G~~~~~--~~~a~G~g~~~~~~~L~  176 (250)
                      +++++.+++.|++++|.++++. +|||+|++||||||++++     |+||.+||+|++.++  +++|+|+|+.+++++||
T Consensus       138 ~isv~~la~~la~~l~~~~~~~-~rp~~v~lLvaG~D~~~g~~~~~p~Ly~iDp~G~~~e~~~~~~AiGsgs~~a~~~Le  216 (294)
T 1q5r_H          138 PLTFDGKANRLASMVRGNLGAA-MQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALK  216 (294)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHH-TTTTCEEEEEEEECTTCSCTTSCEEEEEECSSSCEEECCSSEEEESTTHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhhh-cCCcceEEEEEEEeCCCCcCCCCCEEEEECCCCeEEecCCCeEEEecCcHHHHHHHH
Confidence            9999999999999999888754 899999999999998656     999999999999998  89999999999999999


Q ss_pred             hhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCc--E-----EEEEEEeCCCCceeEEECCHHHHHHHHHHhCCCCccc
Q 025640          177 QDYKDDISREEAVQLALKVLSKTMDSTSLTSDK--L-----ELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQPAA  247 (250)
Q Consensus       177 ~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~--i-----ei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~  247 (250)
                      +.|+++|+++||++++++||..+.++|..+++.  +     +|++|++++     +++++++|++.++..+.+.+.+.
T Consensus       217 ~~y~~~ms~eEAi~la~~aL~~a~~rD~~sG~~~~ir~i~~ev~vI~~~g-----~~~l~~~ei~~~l~~i~~~~~~~  289 (294)
T 1q5r_H          217 KIYSPDSDEETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG-----AVHVSEETTSELARRIVAERTEQ  289 (294)
T ss_dssp             HHCCSSCCHHHHHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETTE-----EEECCHHHHHHHHHHHCC-----
T ss_pred             HhccCCCCHHHHHHHHHHHHHHHHhhccccCCchhhcccCCEEEEEECCC-----EEEcCHHHHHHHHHHHHHHhhhC
Confidence            999999999999999999999999998887654  6     999999876     89999999999999997766543

>3nzj_K Proteasome component PRE2; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_K* 3nzx_K* 4b4t_5

Probab=100.00  E-value=5.5e-47  Score=327.22  Aligned_cols=221  Identities=16%  Similarity=0.205  Sum_probs=193.5

Q ss_pred             CCCCccccc------chHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHH
Q 025640           13 SPEGRLYQV------EYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANIL   86 (250)
Q Consensus        13 ~p~G~l~qv------eya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l   86 (250)
                      +|+.-+-+.      .++.+++.+|+|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+
T Consensus        51 ~p~~~~~~~~~~~~~~~~~~~v~~GtT~vgik~~dGVVlAaD~r~t~G~li~~~~~~KI~~I~d~i~~~~aG~~AD~~~l  130 (287)
T 3nzj_K           51 SPQQFLRAHTDDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFW  130 (287)
T ss_dssp             -------------------------CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECEECHHHHHHH
T ss_pred             CHHHHHHHhcccccccchhhheccCceEEEEEECCEEEEEEccccccCceeecCCcceEEEEcCcEEEEecCCHHHHHHH
Confidence            455555443      26788999999999999999999999999999988888899999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeC
Q 025640           87 INTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGA  166 (250)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~  166 (250)
                      .+.++.++..|++.++++++++.+++.+++++|.+++    +||++++||||||+.+||+||.+||.|++.+++++|+|+
T Consensus       131 ~~~lr~~~~~y~~~~~~~isv~~la~~ls~~l~~~r~----~p~~v~~lvaG~D~~~gp~Ly~iDp~G~~~~~~~~AiGs  206 (287)
T 3nzj_K          131 ETWLGSQCRLHELREKERISVAAASKILSNLVYQYKG----AGLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGS  206 (287)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTT----SCCCEEEEEEEEETTTEEEEEEEETTCCEEECSEEEEST
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhcC----CCceEEEEEEEEcCCCCCEEEEECCCceEEEcCeEEEec
Confidence            9999999999999999999999999999999998865    499999999999976799999999999999999999999


Q ss_pred             ChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhCC
Q 025640          167 NNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGV  242 (250)
Q Consensus       167 g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~  242 (250)
                      |+.+++++||+.|+++||++||++++++||..+.+||..++++++|++|+++|     |++++++||+.++.++.+
T Consensus       207 gs~~a~~~Le~~y~~dms~eEAi~la~~aL~~a~~rD~~sg~~i~V~vItkdg-----~~~l~~~ev~~~l~~~~e  277 (287)
T 3nzj_K          207 GQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDG-----WIYHGNHDVGELFWKVKE  277 (287)
T ss_dssp             THHHHHHHHHTSCCTTCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTE-----EEEEEEEEHHHHHHHHHH
T ss_pred             chHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhCcCCCCceEEEEEeCCC-----EEEeCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999997     899999999998877654

>2jay_A Proteasome; hydrolase; 1.99A {Mycobacterium tuberculosis} PDB: 3mka_C 3mi0_C* 2fhg_H* 2fhh_H 3krd_C* 3mfe_G 3hfa_H* 3h6i_C 3h6f_C 3hf9_H 3mfe_H

Probab=100.00  E-value=1.1e-46  Score=326.13  Aligned_cols=235  Identities=16%  Similarity=0.174  Sum_probs=176.5

Q ss_pred             CCCCCCccccCCCCcc-----cc--cchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEE
Q 025640            3 RRYDSRTTIFSPEGRL-----YQ--VEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACA   75 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l-----~q--veya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~   75 (250)
                      .+|+..+....||.-.     +|  +|||++ +.+|+|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+
T Consensus        23 ~~f~~~~~~~~~~~l~~~~~~~~~~~~ya~~-v~~GtTiVgi~~kdGVVlAaD~r~t~g~li~~~~~~KI~~i~d~i~~~  101 (291)
T 2jay_A           23 SSFTDFLRRQAPELLPASISGGAPLAGGDAQ-LPHGTTIVALKYPGGVVMAGDRRSTQGNMISGRDVRKVYITDDYTATG  101 (291)
T ss_dssp             ------------------------------------CCEEEEEETTEEEEEECCC--------CCCCCCEEEEETTEEEE
T ss_pred             ccHHHHhhhcChhhccccccccCcCcccccc-ccCCcEEEEEEECCEEEEEECCCccCCCeeecCCcccEEEeCCcEEEE
Confidence            3566677777776432     22  699999 999999999999999999999999999888788899999999999999


Q ss_pred             EeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCC-----eEEEEE
Q 025640           76 VAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYG-----FQLYMS  150 (250)
Q Consensus        76 ~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~-----~~Ly~v  150 (250)
                      ++|..+|++.+.+.++.++..|++.++.+++++.+++.+++++|.+++ ..+|||+|++||||||+.++     |+||.+
T Consensus       102 ~aG~~aD~~~l~~~lr~~~~~y~~~~~~~i~v~~la~~la~~l~~~~~-~~~rpf~v~~lvaG~D~~g~~~~~~p~Ly~i  180 (291)
T 2jay_A          102 IAGTAAVAVEFARLYAVELEHYEKLEGVPLTFAGKINRLAIMVRGNLA-AAMQGLLALPLLAGYDIHASDPQSAGRIVSF  180 (291)
T ss_dssp             EESCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHTCHH-HHHHTCCCEEEEEEECTTCSCSTTCEEEEEE
T ss_pred             EcccHHHHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHHHHHHhhh-hhccccceeEEEEEEeCCCCcCCCCCEEEEE
Confidence            999999999999999999999999999999999999999999998865 35789999999999998656     999999


Q ss_pred             CCCCcee--cceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCc--E-----EEEEEEeCCCC
Q 025640          151 DPSGNYG--GWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDK--L-----ELAEVFLMPSG  221 (250)
Q Consensus       151 d~~G~~~--~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~--i-----ei~ii~~~~~~  221 (250)
                      ||+|++.  +++++|+|+|+.+++++||+.|+++|+++||++++++||..+.++|..+++.  +     +|++|++++  
T Consensus       181 Dp~G~~~e~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eEAi~la~~aL~~a~~~D~~sg~~e~vr~~~~~v~vi~~dg--  258 (291)
T 2jay_A          181 DAAGGWNIEEEGYQAVGSGSLFAKSSMKKLYSQVTDGDSGLRVAVEALYDAADDDSATGGPDLVRGIFPTAVIIDADG--  258 (291)
T ss_dssp             CTTSCEEECSSSEEEESTTHHHHHHHHHHHGGGCCSHHHHHHHHHHHHHHC----------------CCEEEEEETTE--
T ss_pred             CCCCcEEecCCCEEEEecCHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhhCCCCCCcccccccCCEEEEEECCC--
Confidence            9999998  8999999999999999999999999999999999999999999998877764  2     699999986  


Q ss_pred             ceeEEECCHHHHHHHHHHhCCCC
Q 025640          222 KVKYQVCSPEALSKLLVKHGVTQ  244 (250)
Q Consensus       222 ~~~~~~~~~~ei~~~~~~~~~~~  244 (250)
                         +++++++||+.++..+.+.+
T Consensus       259 ---~~~l~~~ei~~~~~~~~~~~  278 (291)
T 2jay_A          259 ---AVDVPESRIAELARAIIESR  278 (291)
T ss_dssp             ---EEECCHHHHHHHHHHC----
T ss_pred             ---eEEcCHHHHHHHHHHHHHhh
Confidence               89999999999999886554

>1iru_L 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_K* 3une_K 3unf_K* 3unh_K

Probab=100.00  E-value=6.3e-46  Score=306.90  Aligned_cols=203  Identities=19%  Similarity=0.273  Sum_probs=192.0

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|.++.+++.+||++|++|++|+++|..+|++.+.+.++.++..|++.++.+++++.++
T Consensus         1 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (204)
T 1iru_L            1 TTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAAS   80 (204)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CeEEEEEeCCEEEEEEcCCcccCCEEEcCcccceEEcCCCEEEEccCcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            58999999999999999999998777777899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.+|.+++    +|+++++||||||+ .||+||.+||+|++.+++++|+|+|+.+++++||+.|+++||++||+++
T Consensus        81 ~~l~~~~~~~r~----~~~~v~~lvaG~D~-~gp~Ly~idp~G~~~~~~~~aiG~gs~~a~~~Le~~~~~~~s~eea~~l  155 (204)
T 1iru_L           81 KLLANMVYQYKG----MGLSMGTMICGWDK-RGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDL  155 (204)
T ss_dssp             HHHHHHHHTTTT----SCCCBEEEEEEECS-SSEEEEEEESSSCEEECSEEEESTTHHHHHHHHHTTCCTTCCHHHHHHH
T ss_pred             HHHHHHHHHhCC----CCeeEEEEEEEEeC-CCCEEEEECCCCcEEEeCCEEEEcCHHHHHHHHhccCCCCCCHHHHHHH
Confidence            999999998754    58999999999998 5899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhCCCC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQ  244 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~~~  244 (250)
                      +++||..+.+|+..++++++|++|++++     ++.++++|++.++..+.+.+
T Consensus       156 ~~~al~~~~~rd~~s~~~i~v~vi~~~g-----~~~l~~~ei~~~~~~~~~~~  203 (204)
T 1iru_L          156 ARRAIYQATYRDAYSGGAVNLYHVREDG-----WIRVSSDNVADLHEKYSGST  203 (204)
T ss_dssp             HHHHHHHHHHHBTTCCSEEEEEEECSSC-----EEEEEEEEHHHHHHHHTC--
T ss_pred             HHHHHHHHHHhCccCCCceEEEEEeCCc-----eEEeCHHHHHHHHHHhccCC
Confidence            9999999999999999999999999876     89999999999999986543

>1ryp_L 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_L 1vsy_L 1z7q_L 3l5q_P 1g65_K* 1g0u_K* 1jd2_K* 2f16_K* 2fak_K* 2fny_K* 2gpl_K* 2zcy_K* 3bdm_K* 3d29_K* 3dy3_K* 3dy4_K* 3e47_K* 3gpj_K* 3gpt_K* 3gpw_K* ...

Probab=100.00  E-value=4e-46  Score=309.85  Aligned_cols=202  Identities=15%  Similarity=0.213  Sum_probs=192.0

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|.++.+++.+||++|++|++|+++|..+|++.+.+.++.++..|++.++.+++++.++
T Consensus         1 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (212)
T 1ryp_L            1 TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAAS   80 (212)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CcEEEEEeCCEEEEEEcCCcccCCeEecCcccceeeeCCcEEEEccccHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            58999999999999999999998777777899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.+|.+++    .||++++||||||++.+|+||.+||+|++.+++++|+|+|+.+++++||+.|+++||++||+++
T Consensus        81 ~~l~~~~~~~~~----~p~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~s~eea~~l  156 (212)
T 1ryp_L           81 KILSNLVYQYKG----AGLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYL  156 (212)
T ss_dssp             HHHHHHHHHTTT----SCCCBEEEEEEEETTTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHHHCCTTCCHHHHHHH
T ss_pred             HHHHHHHHhhCC----CCceEEEEEEEEeCCCCCEEEEEcCCceeEecCCEEEcCCHHHHHHHHHhhCCCCCCHHHHHHH
Confidence            999999999876    3999999999999656899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhCC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGV  242 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~  242 (250)
                      +++||..+.+|+..++++++|++|++++     +++++++||+.++.++.+
T Consensus       157 a~~al~~~~~rd~~s~~~i~v~vi~~~g-----~~~~~~~ei~~~~~~~~~  202 (212)
T 1ryp_L          157 GKRSILAAAHRDAYSGGSVNLYHVTEDG-----WIYHGNHDVGELFWKVKE  202 (212)
T ss_dssp             HHHHHHHHHHHBTTCCSEEEEEEEETTE-----EEEEEEEEHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccccCCceEEEEEcCCc-----eEEECHHHHHHHHHHHHH
Confidence            9999999999999999999999999876     899999999999877754

>1q5q_H Proteasome beta-type subunit 1; proteasome assembly, Pro-peptide, inter-subunit contacts, RH erythropolis, hydrolase; 2.60A {Rhodococcus erythropolis} SCOP: d.153.1.4

Probab=100.00  E-value=1.1e-45  Score=311.80  Aligned_cols=211  Identities=22%  Similarity=0.246  Sum_probs=195.4

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++.+++++.++
T Consensus         1 tT~vgi~~~dgVVlaaD~r~~~g~l~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (235)
T 1q5q_H            1 TTIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKA   80 (235)
T ss_dssp             CCEEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEECCCCCcCCEEecCCcCcEEEeCCcEEEEcCCcHHHHHHHHHHHHHHHHHhHHHhCCCCCHHHHH
Confidence            58999999999999999999998777777899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCC-----eEEEEECCCCceecc--eEEEEeCChHHHHHHHHhhCCCCCC
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYG-----FQLYMSDPSGNYGGW--KAAAIGANNQAAQSILKQDYKDDIS  184 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~-----~~Ly~vd~~G~~~~~--~~~a~G~g~~~~~~~L~~~~~~~~s  184 (250)
                      +.|++++|.++++. +|||++++||||||++++     |+||.+||+|++.++  +++|+|+|+.+++++||+.|+++||
T Consensus        81 ~~l~~~~~~~~~~~-~rp~~v~~lvaG~D~~~g~~~~~p~Ly~idp~G~~~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms  159 (235)
T 1q5q_H           81 NRLASMVRGNLGAA-MQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSD  159 (235)
T ss_dssp             HHHHHHHHTTHHHH-TTTCCEEEEEEEECTTCSSTTSCEEEEEECTTSCEEECCSSEEEESTTHHHHHHHHHHHCCTTCC
T ss_pred             HHHHHHHHHHHHhh-hcccceEEEEEEEECCCCccCCCCEEEEECCCCceEEeCCCeEEECCCHHHHHHHHHhhcCCCCC
Confidence            99999999988764 899999999999998657     999999999999999  9999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCc--E-----EEEEEEeCCCCceeEEECCHHHHHHHHHHhCCCCcccc
Q 025640          185 REEAVQLALKVLSKTMDSTSLTSDK--L-----ELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQPAAE  248 (250)
Q Consensus       185 ~~ea~~l~~~~l~~~~~~~~~~~~~--i-----ei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~~~  248 (250)
                      ++||++++++||..+.+++..+++.  +     +|++|++++     ++.++++|+++++..+.+.+.+++
T Consensus       160 ~eeA~~la~~al~~a~~~d~~sg~~~~i~~~~~ev~vi~~~g-----~~~l~~~ei~~~~~~~~~~~~~~~  225 (235)
T 1q5q_H          160 EETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG-----AVHVSEETTSELARRIVAERTEQG  225 (235)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETTE-----EEECCHHHHHHHHHHHHHHHHTC-
T ss_pred             HHHHHHHHHHHHHHHHhhCcccCCcccccccccEEEEEeCCC-----eEEeCHHHHHHHHHHHHHHHhhCC
Confidence            9999999999999999999887753  2     999999876     899999999999998866555443

>1iru_H 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_N* 3une_N

Probab=100.00  E-value=5.6e-46  Score=307.42  Aligned_cols=200  Identities=20%  Similarity=0.291  Sum_probs=189.4

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|.++.+++.+||++|++|++|+++|..+|++.+.+.++.++..|++.++++++++.++
T Consensus         1 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (205)
T 1iru_H            1 TTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAA   80 (205)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             CcEEEEEeCCEEEEEEcCCcccCcEEecCCcCceEEcCCCEEEEcCccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            58999999999999999999999777777889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.+|.+++     ||++++||||||+++||+||.+||.|++.+++++++|+|+.+++++||+.|+++||++||+++
T Consensus        81 ~~l~~~~~~~~~-----p~~~~~lvaG~D~~~gp~ly~~d~~G~~~~~~~~a~Gsgs~~a~~~Le~~~~~~~s~eea~~l  155 (205)
T 1iru_H           81 SLFKEMCYRYRE-----DLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQF  155 (205)
T ss_dssp             HHHHHHHHHTTT-----TCCEEEEEEEEETTTEEEEEEECTTSCCEECSEEEESGGGGGGHHHHHHHCCTTCCHHHHHHH
T ss_pred             HHHHHHHHhcCc-----CccEEEEEEEEeCCCCCEEEEECCCCcEEecCEEEECCCHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            999999998864     999999999999866899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      +++||..+.+++..++++++|++|++++   ..++.++++||+.+++.
T Consensus       156 ~~~al~~~~~~d~~s~~~i~v~vi~~~g---~~~~~l~~~ei~~~~~~  200 (205)
T 1iru_H          156 TANALALAMERDGSSGGVIRLAAIAESG---VERQVLLGDQIPKFAVA  200 (205)
T ss_dssp             HHHHHHHHHHHBTTCCSCEEEEEEETTE---EEEEEECGGGSCCCCCC
T ss_pred             HHHHHHHHHHhccccCCcEEEEEEeCCC---eEEEEeChHHhhHHHhh
Confidence            9999999999999999999999999986   35789999999877654

>1ryp_N 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_N* 1jd2_M* 1g65_M 1vsy_N 1z7q_N 2f16_M* 2fak_M* 2fny_M* 2gpl_M* 3d29_M* 3dy3_M* 3dy4_M* 3e47_M* 3gpj_M* 3gpt_M* 3gpw_M* 3hye_M* 3l5q_R 3mg0_M* 3mg4_M* ...

Probab=100.00  E-value=1.1e-46  Score=317.49  Aligned_cols=209  Identities=13%  Similarity=0.121  Sum_probs=195.7

Q ss_pred             HHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHH-----
Q 025640           25 MEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTY-----   99 (250)
Q Consensus        25 ~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~-----   99 (250)
                      .+++.+|+|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++     
T Consensus         2 ~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~   81 (233)
T 1ryp_N            2 QQPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLA   81 (233)
T ss_dssp             CCCCEEECCEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTT
T ss_pred             cccccCCceEEEEEECCEEEEEEcCccccCCeeecCCcCceEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHhhccchh
Confidence            367899999999999999999999999998888778899999999999999999999999999999999999998     


Q ss_pred             HhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhC
Q 025640          100 AYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDY  179 (250)
Q Consensus       100 ~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~  179 (250)
                      .++.+++++.+++.+++.++.  ++.+.|||++++||||||++++|+||.+||.|++.+++++++|+|+.+++++||+.|
T Consensus        82 ~~~~~~~v~~la~~l~~~ly~--~r~~~~P~~v~~lvaG~D~~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~  159 (233)
T 1ryp_N           82 DAEEALEPSYIFEYLATVMYQ--RRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVV  159 (233)
T ss_dssp             TTTTSCCHHHHHHHHHHHHHH--HHHTTCCCCEEEEEEEECTTSCEEEEEEETTCCEECCSEEECTHHHHHHHHHHTTTC
T ss_pred             hcCCCCCHHHHHHHHHHHHHH--hcCCCCCceEEEEEEEEcCCCCEEEEEECCCcCeEEcCEEEECcCHHHHHHHHHHhh
Confidence            899999999999999999854  555689999999999999866899999999999999999999999999999999999


Q ss_pred             CC-----CCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeC-CCCceeEEECCHHHHHHH-HHHh
Q 025640          180 KD-----DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLM-PSGKVKYQVCSPEALSKL-LVKH  240 (250)
Q Consensus       180 ~~-----~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~-~~~~~~~~~~~~~ei~~~-~~~~  240 (250)
                      ++     +||++||++++++||..+.+|+..++++++|++|+++ +     ++.++++||+.+ |.-.
T Consensus       160 ~~~~~~~~ms~eea~~la~~al~~~~~rd~~sg~~i~v~vi~~~~g-----~~~~~~~~i~~~~w~~~  222 (233)
T 1ryp_N          160 DRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTG-----LTFKKNLQVENMKWDFA  222 (233)
T ss_dssp             SSGGGGGGCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTTE-----EEEEEEEECCSCCCGGG
T ss_pred             ccccccCCCCHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEECCCC-----eEEcChHhcccccchhh
Confidence            99     9999999999999999999999999999999999998 5     889999998877 6433

>1iru_N 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_M* 3une_M 3unf_M* 3unh_M

Probab=100.00  E-value=2.5e-46  Score=312.51  Aligned_cols=206  Identities=13%  Similarity=0.111  Sum_probs=193.4

Q ss_pred             HHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHH-HhCC
Q 025640           25 MEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTY-AYQE  103 (250)
Q Consensus        25 ~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~-~~~~  103 (250)
                      .+|+.+|+|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++ .++.
T Consensus         2 ~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~   81 (219)
T 1iru_N            2 QNPMVTGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGH   81 (219)
T ss_dssp             CSCCSEECCCEEEEETTEEEEEEECCEEETTEEEECSCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCSSC
T ss_pred             CCCccCCceEEEEEeCCEEEEEECCccccCcEEecCCCCceEEeCCCEEEEeccCHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            368899999999999999999999999998888778899999999999999999999999999999999999998 8999


Q ss_pred             CCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCC--
Q 025640          104 PMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD--  181 (250)
Q Consensus       104 ~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~--  181 (250)
                      +++++.+++.+++.++.  ++.+.|||++++||||||+. +|+||.+||.|++.+++++++|+|+++++++||+.|++  
T Consensus        82 ~~~v~~la~~l~~~ly~--~r~~~~P~~v~~lvaG~D~~-gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~  158 (219)
T 1iru_N           82 SYSPRAIHSWLTRAMYS--RRSKMNPLWNTMVIGGYADG-ESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQP  158 (219)
T ss_dssp             CCCHHHHHHHHHHHHHH--HHHTTCCCCEEEEEEEEETT-EEEEEEECSSCCEEECSEEECTTHHHHTHHHHHHHHTSCS
T ss_pred             CCCHHHHHHHHHHHHHH--hcccCCCceEEEEEEEEECC-CCEEEEECCCCCeEECCeEEECccHHHHHHHHHhhcCCCC
Confidence            99999999999999864  45578999999999999984 99999999999999999999999999999999999999  


Q ss_pred             CCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 025640          182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLV  238 (250)
Q Consensus       182 ~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~  238 (250)
                      +||++||++++++||..+.+++..++++++|++|++++     ++.++++||+..|.
T Consensus       159 ~mt~eea~~l~~~al~~~~~~d~~sg~~i~v~vi~~~g-----~~~~~~~~i~~~~~  210 (219)
T 1iru_N          159 VLSQTEARDLVERCMRVLYYRDARSYNRFQTATVTEKG-----VEIEGPLSTETNWD  210 (219)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTE-----EEEEEEECCCCCCG
T ss_pred             CCCHHHHHHHHHHHHHHHHHhcCcCCCcEEEEEEcCCC-----EEEcCCeeccchhh
Confidence            99999999999999999999999999999999999986     78999888876653

>1ryp_H 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 3nzj_N* 3nzw_N* 3nzx_N* 1vsy_H 3l5q_B 1g65_N* 1fnt_H 1g0u_N* 1jd2_N* 1z7q_H 2f16_N* 2fak_N* 2fny_N* 2gpl_N* 2zcy_N* 3bdm_N* 3d29_N* 3dy3_N* 3dy4_N* 3e47_N* ...

Probab=100.00  E-value=9.6e-45  Score=300.04  Aligned_cols=189  Identities=16%  Similarity=0.268  Sum_probs=181.4

Q ss_pred             HHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCC
Q 025640           25 MEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEP  104 (250)
Q Consensus        25 ~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~  104 (250)
                      .+++++|+|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.+++ 
T Consensus         3 ~~av~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~-   81 (205)
T 1ryp_H            3 KGEVSLGASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGT-   81 (205)
T ss_dssp             TTCCBCCCCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSS-
T ss_pred             CCCCcCCceEEEEEeCCEEEEEEcCCcccCcEEEcCCcCceEEcCCCEEEEccCCHHHHHHHHHHHHHHHHHHHHHhCC-
Confidence            5889999999999999999999999999997777778899999999999999999999999999999999999999999 


Q ss_pred             CCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCC
Q 025640          105 MPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDIS  184 (250)
Q Consensus       105 ~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s  184 (250)
                      ++++.+++.+++.+|.++++     |++++||||||+..||+||.+||.|++.+++++|+|+|+.+++++||+.|+++||
T Consensus        82 ~~v~~la~~l~~~~~~~~~~-----~~~~~lvaG~D~~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~s  156 (205)
T 1ryp_H           82 PSTETAASVFKELCYENKDN-----LTAGIIVAGYDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMS  156 (205)
T ss_dssp             CCHHHHHHHHHHHHHHTTTT-----CCEEEEEEEEETTTEEEEEEECTTSCCEEESEEEESGGGGGGHHHHHHHCCTTCC
T ss_pred             CCHHHHHHHHHHHHHhhhcC-----ceEEEEEEEEecCCCcEEEEECCCccEEecCEEEEEecHHHHHHHHHhccCCCCC
Confidence            99999999999999998652     9999999999986689999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          185 REEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       185 ~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      ++||++++++||..+.+|+..++++++|++|++++
T Consensus       157 ~eea~~l~~~al~~a~~~d~~sg~~i~v~vi~~~g  191 (205)
T 1ryp_H          157 KEETVDFIKHSLSQAIKWDGSSGGVIRMVVLTAAG  191 (205)
T ss_dssp             HHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTE
T ss_pred             HHHHHHHHHHHHHHHHHhCCccCCeEEEEEEcCCC
Confidence            99999999999999999999999999999999987

>1iru_M 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_L* 3une_L 3unf_L* 3unh_L

Probab=100.00  E-value=2.6e-44  Score=299.06  Aligned_cols=188  Identities=19%  Similarity=0.264  Sum_probs=179.8

Q ss_pred             hcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCH
Q 025640           28 IGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPV  107 (250)
Q Consensus        28 ~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~  107 (250)
                      +++|+|+|||+++||||||+|+|.++|+++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++.++++
T Consensus         6 v~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v   85 (213)
T 1iru_M            6 VFNGGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTT   85 (213)
T ss_dssp             CCCCCEEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCH
T ss_pred             cCCCCcEEEEEeCCEEEEEECCCcccCCEEecCCCCcEEEcCCCEEEEccccHHHHHHHHHHHHHHHHHHHHhcCCCCCH
Confidence            57999999999999999999999999999887889999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhh---------
Q 025640          108 EQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQD---------  178 (250)
Q Consensus       108 ~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~---------  178 (250)
                      +.+++.+++.++  +++  .|||++++||||||++++|+||.+||.|++.+++++|+|+|+.+++++||+.         
T Consensus        86 ~~la~~l~~~~y--~~r--~~P~~v~~lvaG~D~~g~p~Ly~id~~G~~~~~~~~aiGsg~~~a~~~Le~~~~~~~~~~~  161 (213)
T 1iru_M           86 GAIAAMLSTILY--SRR--FFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNV  161 (213)
T ss_dssp             HHHHHHHHHHHH--HTT--TSCCCEEEEEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTTCCSCSSC
T ss_pred             HHHHHHHHHHHH--hhC--CCCceEEEEEEEEcCCCCEEEEEECCCCCEEECCEEEEeeCHHHHHHHHhhcccccccccc
Confidence            999999999985  443  7999999999999986679999999999999999999999999999999999         


Q ss_pred             CCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          179 YKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       179 ~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      |+++||++||++++++||..+.+++..++++++|++|++++
T Consensus       162 ~~~~~s~eea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g  202 (213)
T 1iru_M          162 EHVPLSLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEG  202 (213)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHHBTTSCSEEEEEEEETTE
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHhCCccCCcEEEEEEcCCC
Confidence            88999999999999999999999999999999999999987

>1ryp_K 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_K 1g0u_J* 1jd2_J* 1g65_J 1vsy_K 1z7q_K 2f16_J* 2fak_J* 2fny_J* 2gpl_J* 2zcy_J* 3bdm_J* 3d29_J* 3dy3_J* 3dy4_J* 3e47_J* 3gpj_J* 3gpt_J* 3gpw_J* 3hye_J* ...

Probab=100.00  E-value=1.7e-44  Score=297.01  Aligned_cols=192  Identities=19%  Similarity=0.215  Sum_probs=181.5

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|+++.+++.+||++|++|++|+++|..+|++.+.+.++.++..|++.++++++++.++
T Consensus         2 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   81 (198)
T 1ryp_K            2 DIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVS   81 (198)
T ss_dssp             CCEEEEECSSCEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             ceEEEEEECCEEEEEECCCcccCCEEEecCCCceEEeCCCEEEEeccCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            78999999999999999999999998877899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeC-CCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDK-NYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQ  190 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~-~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~  190 (250)
                      +.+++.++.+++.  .+||++++||||||+ +++|+||.+||+|++.+++++|+|+|+++++++||+.|+++||++||++
T Consensus        82 ~~l~~~l~~~~~~--r~p~~v~~lvaG~D~~~~~p~Ly~idp~G~~~~~~~~aiG~g~~~a~~~Le~~~~~~~s~eea~~  159 (198)
T 1ryp_K           82 SFVRQELAKSIRS--RRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLD  159 (198)
T ss_dssp             HHHHHHHHHHTTS--SSCCCEEEEEEEEETTTTEEEEEEECTTCCEEECSEEECTTHHHHHHHHHHHHCCTTCCHHHHHH
T ss_pred             HHHHHHHHHhccc--CCCceEEEEEEEEeCCCCCcEEEEECCCCCEEECCEEEEcccHHHHHHHHHhhcCCCCCHHHHHH
Confidence            9999999887642  359999999999997 4689999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCH
Q 025640          191 LALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSP  230 (250)
Q Consensus       191 l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~  230 (250)
                      ++++||..+.+++..++++++|++|++++     ++.+++
T Consensus       160 l~~~al~~~~~~d~~s~~~i~v~vi~~~g-----~~~~~~  194 (198)
T 1ryp_K          160 LLKLCVQELEKRMPMDFKGVIVKIVDKDG-----IRQVDD  194 (198)
T ss_dssp             HHHHHHHHHHHHCSBCCCCEEEEEEETTE-----EEEECC
T ss_pred             HHHHHHHHHHHhCccCCCceEEEEEcCCC-----EEEecc
Confidence            99999999999999999999999999986     666654

>1g0u_M Proteasome component PRE4; ubiquitin, degradation, protease, NTN-hydrolase; 2.40A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 2zcy_M* 3bdm_M* 3mg6_M* 3mg7_M* 3mg8_M* 3nzj_M* 3nzw_M* 3nzx_M*

Probab=100.00  E-value=6.1e-46  Score=318.51  Aligned_cols=215  Identities=13%  Similarity=0.114  Sum_probs=197.6

Q ss_pred             ccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHH
Q 025640           20 QVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTY   99 (250)
Q Consensus        20 qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~   99 (250)
                      ..+.+.+++.+|+|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.|.+.++.++..|++
T Consensus        30 ~~~~~~~av~~GtT~vgi~~~dgVVlAaD~r~t~g~~i~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~lr~~~~~~~~  109 (266)
T 1g0u_M           30 PMVNTQQPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAY  109 (266)
T ss_dssp             ----CCCCCEEECCEEEEEETTEEEEEEECCEEETTEEEECCCCCEEECTTSEEEEEEEEHHHHHHHHHHHHHHHHHHHT
T ss_pred             chhhhccCcccCceEEEEEECCEEEEEEcCCcccCceeecCCcCcEEEcCCCEEEEeccCHHHHHHHHHHHHHHHHHhhh
Confidence            35677889999999999999999999999999998888778899999999999999999999999999999999999998


Q ss_pred             -----HhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHH
Q 025640          100 -----AYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSI  174 (250)
Q Consensus       100 -----~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~  174 (250)
                           .++.+++++.+++.+++.++.  ++.+.|||++++||||||++++|+||.+||.|++.+++++|+|+|+.+++++
T Consensus       110 ~~~~~~~~~~~~v~~la~~l~~~ly~--~r~~~~P~~v~~lvaG~D~~~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~  187 (266)
T 1g0u_M          110 DNPLADAEEALEPSYIFEYLATVMYQ--RRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPL  187 (266)
T ss_dssp             TCTTTTTTTSCCHHHHHHHHHHHHHH--HHHTTCCCCEEEEEEEECTTSCEEEEEEETTCCEECCSEEECTHHHHTHHHH
T ss_pred             ccchhhcCCCCCHHHHHHHHHHHHHH--hccCCCCceEEEEEEEEcCCCCEEEEEECCCCCEEeCCEEEEccCHHHHHHH
Confidence                 899999999999999999854  5556899999999999998668999999999999999999999999999999


Q ss_pred             HHhhCCC-----CCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeC-CCCceeEEECCHHHHHHH-HHHhC
Q 025640          175 LKQDYKD-----DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLM-PSGKVKYQVCSPEALSKL-LVKHG  241 (250)
Q Consensus       175 L~~~~~~-----~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~-~~~~~~~~~~~~~ei~~~-~~~~~  241 (250)
                      ||+.|++     +||++||++++++||..+.+|+..++++++|++|+++ +     ++.++++||+.+ |.-.+
T Consensus       188 Le~~~~~~~~~~~ms~eeA~~la~~al~~a~~rd~~sg~~i~v~vI~k~~g-----~~~~~~~ei~~~~w~~~~  256 (266)
T 1g0u_M          188 LRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTG-----LTFKKNLQVENMKWDFAK  256 (266)
T ss_dssp             HTTTCSSGGGGGGCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTTE-----EEEEEEEECCCCCCGGGG
T ss_pred             HHHhhcccccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCcEEEEEEECCCC-----eEEcCHHHhhhhhhhHHh
Confidence            9999999     9999999999999999999999999999999999998 5     889999988877 64433

>3unf_H Proteasome subunit beta type-10; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_H

Probab=100.00  E-value=2.4e-44  Score=302.93  Aligned_cols=194  Identities=20%  Similarity=0.291  Sum_probs=184.5

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|+++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++++++++.++
T Consensus         1 TT~vgi~~kdgVVlaaD~r~t~g~~v~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (234)
T 3unf_H            1 TTIAGLVFRDGVILGADTRATNDSVVADKSCEKIHFIAPKIYCCGAGVAADTEMTTRMAASKMELHALSTGREPRVATVT   80 (234)
T ss_dssp             CEEEEEECSSEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHH
T ss_pred             CeEEEEEeCCEEEEEECCCcccCCEeccCccccEEEecCCEEEEecccHHHHHHHHHHHHHHHHhhHHhcCCCCCHHHHH
Confidence            68999999999999999999999988888899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.++.+     .+||++++||||||+ .||+||.+||.|++.+++++|+|+|+.+++++||+.|+++|+++||+++
T Consensus        81 ~~l~~~l~~~-----~~p~~v~llvaG~D~-~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eeA~~l  154 (234)
T 3unf_H           81 RILRQTLFRY-----QGHVGASLVVGGVDL-NGPQLYEVHPHGSYSRLPFTALGSGQGAAVALLEDRFQPNMTLEAAQEL  154 (234)
T ss_dssp             HHHHHHHHHT-----TTCSCEEEEEEEEET-TEEEEEEECTTSCEEECSEEEEETTHHHHHHHHHHHCCSSCCHHHHHHH
T ss_pred             HHHHHHHHhc-----CCCccEEEEEEEEeC-CCCEEEEECCCCCEEeccEEEEcCCchhhHHHHHhccCCCCCHHHHHHH
Confidence            9999998865     369999999999998 4899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHH
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKL  236 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~  236 (250)
                      +++||..+.++|..++++++|++|+++|     ++.+.+++++.-
T Consensus       155 a~~al~~~~~~D~~sg~~iev~vi~~dg-----~~~l~~~~i~~~  194 (234)
T 3unf_H          155 LVEAITAGILSDLGSGGNVDACVITAGG-----AKLQRALSTPTE  194 (234)
T ss_dssp             HHHHHHHHHHHBTTCCSCEEEEEEESSC-----EEEEEEEECCCC
T ss_pred             HHHHHHHHHhhcCCCCCcEEEEEEECCC-----EEEeCceecccc
Confidence            9999999999999999999999999997     788888887643

>1iru_J 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_I* 3une_I 3unf_I* 3unh_I

Probab=100.00  E-value=1.5e-43  Score=292.92  Aligned_cols=188  Identities=11%  Similarity=0.158  Sum_probs=177.4

Q ss_pred             hcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCH
Q 025640           28 IGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPV  107 (250)
Q Consensus        28 ~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~  107 (250)
                      +.+|+|+|||+++||||||+|+|.++|+++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++.++++
T Consensus         5 ~~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v   84 (205)
T 1iru_J            5 SYNGGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIKP   84 (205)
T ss_dssp             TSSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEECSTTEEEECCSCHHHHHHHHHHHHHHHHHHHHHSSSCCCH
T ss_pred             cCCCCeEEEEEeCCEEEEEECCccccCCeEeecCCccEEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHHhhcCCCCCH
Confidence            47899999999999999999999999999988889999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhccccCCCcceeEEEEEEEEeC-CCCeEEEEECCCCceecc-eEEEEeCChHHHHHHHHhhCCCCCCH
Q 025640          108 EQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDK-NYGFQLYMSDPSGNYGGW-KAAAIGANNQAAQSILKQDYKDDISR  185 (250)
Q Consensus       108 ~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~-~~~~~Ly~vd~~G~~~~~-~~~a~G~g~~~~~~~L~~~~~~~~s~  185 (250)
                      +.+++.+++.++  +++  ..||++++||||||+ +++|+||.+||.|++.++ +++++|+|+++++++||+.|+++||+
T Consensus        85 ~~la~~l~~~~y--~~r--~~P~~v~~lvaG~D~~~~~p~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~~~~~s~  160 (205)
T 1iru_J           85 YTLMSMVANLLY--EKR--FGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDP  160 (205)
T ss_dssp             HHHHHHHHHHHH--TTT--TSCCSCCCEEEEECTTSCCEEEEEECTTCCEEECSSEEEEETTHHHHHHHHHHHCCSSCCH
T ss_pred             HHHHHHHHHHHH--Hhc--CCCceEEEEEEEEeCCCCCeEEEEECCCCCccccCCeeEeeeCHHHHHHHHhcccCCCCCH
Confidence            999999999984  444  349999999999996 468999999999998654 67999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          186 EEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       186 ~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      +||++++++||..+.+++..++++++|++|++++
T Consensus       161 eea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g  194 (205)
T 1iru_J          161 DHLFETISQAMLNAVDRDAVSGMGVIVHIIEKDK  194 (205)
T ss_dssp             HHHHHHHHHHHHHHGGGBTTSCSCEEEEEEESSB
T ss_pred             HHHHHHHHHHHHHHHHhCcccCCceEEEEEcCCC
Confidence            9999999999999999999999999999999987

>1ryp_J 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_I* 1g65_I 1vsy_J 2f16_I* 2fak_I* 2fny_I* 2gpl_I* 3d29_I* 3dy3_I* 3dy4_I* 3e47_I* 3gpj_I* 3gpt_I* 3gpw_I* 3hye_I* 3l5q_N 3mg0_I* 3mg4_I* 3oeu_I* 3oev_I* ...

Probab=100.00  E-value=2.9e-43  Score=290.89  Aligned_cols=188  Identities=17%  Similarity=0.194  Sum_probs=177.2

Q ss_pred             HhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCC
Q 025640           27 AIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMP  106 (250)
Q Consensus        27 a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~  106 (250)
                      .+.+|+|+|||+++||||||+|+|.++++++.+++.+||++|+ +++|+++|..+|++.+.+.++.++..|++.++.+++
T Consensus         4 ~~~~Gtt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~-~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~   82 (204)
T 1ryp_J            4 SSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYG-HVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIE   82 (204)
T ss_dssp             GGSSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEEET-TEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCC
T ss_pred             cCCCCCeEEEEEeCCEEEEEEcCCcccCCEEeeCCcceEEEeC-CEEEEeeEcHHHHHHHHHHHHHHHHHHhhccCCCCC
Confidence            4679999999999999999999999999999888899999999 999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeC-CCCeEEEEECCCCceecc-eEEEEeCChHHHHHHHHhhCCCCCC
Q 025640          107 VEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDK-NYGFQLYMSDPSGNYGGW-KAAAIGANNQAAQSILKQDYKDDIS  184 (250)
Q Consensus       107 ~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~-~~~~~Ly~vd~~G~~~~~-~~~a~G~g~~~~~~~L~~~~~~~~s  184 (250)
                      ++.+++.+++.+  |+++  ..||++++||||||+ +++|+||.+||.|++.++ +++++|+|+++++++||+.|+++||
T Consensus        83 v~~la~~l~~~~--y~~~--~~P~~v~~lvaG~D~~~~gp~Ly~idp~G~~~~~~~~~aiG~gs~~a~~~Le~~~~~~~s  158 (204)
T 1ryp_J           83 PETFTQLVSSSL--YERR--FGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLE  158 (204)
T ss_dssp             HHHHHHHHHHHH--HTTT--TSCCCEEEEEEEECTTTCCEEEEEECTTCCEECCSSEEEEETTHHHHHHHHHHHCCSSCC
T ss_pred             HHHHHHHHHHHH--HHhc--CCCceEEEEEEEEeCCCCceEEEEECCCCCccccCceeEeccCHHHHHHHHhhhcCCCcC
Confidence            999999999998  4554  349999999999996 468999999999998655 6799999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          185 REEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       185 ~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      ++||++++++||..+.+++..++++++|++|++++
T Consensus       159 ~eea~~l~~~al~~~~~~d~~s~~~i~v~vi~~~g  193 (204)
T 1ryp_J          159 PEDLFETISQALLNAADRDALSGWGAVVYIIKKDE  193 (204)
T ss_dssp             HHHHHHHHHHHHHHHHTTBTTSCSCEEEEEEESSC
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCcEEEEEEcCCC
Confidence            99999999999999999999999999999999987

>3nzj_H Proteasome component PUP1; ubiquitin, protein degradation, N-terminal nucleophilic HYDR 19S regulatory particle; HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB: 3nzw_H* 3nzx_H* 4b4t_2

Probab=100.00  E-value=1.1e-43  Score=303.13  Aligned_cols=189  Identities=19%  Similarity=0.265  Sum_probs=175.6

Q ss_pred             HHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCC
Q 025640           25 MEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEP  104 (250)
Q Consensus        25 ~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~  104 (250)
                      .||+++|+|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++++
T Consensus        23 ~kav~~GtTivgi~~kdGVVlAaD~r~t~g~li~~~~~~KI~~I~d~i~~~~aG~~aD~~~l~~~lr~~~~~~~~~~~~~  102 (261)
T 3nzj_H           23 PKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSRE  102 (261)
T ss_dssp             -------CCEEEEEETTEEEEEEECCEEETTEEEETTCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSC
T ss_pred             CcccccCceEEEEEECCEEEEEEcCCcccCCeeccCCcceEEEEcCCEEEEeccCHHHHHHHHHHHHHHHHHhHHhhCCC
Confidence            58999999999999999999999999999988888899999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCC
Q 025640          105 MPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDIS  184 (250)
Q Consensus       105 ~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s  184 (250)
                      ++++.+++.+++.++.+     .+||++++||||||+ .||+||.+||.|++.+++++|+|+|+.+++++||+.|+++|+
T Consensus       103 ~~v~~~a~~l~~~l~~~-----~~~~gv~llvaG~D~-~Gp~Ly~iDp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms  176 (261)
T 3nzj_H          103 PRVVSALQMLKQHLFKY-----QGHIGAYLIVAGVDP-TGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLT  176 (261)
T ss_dssp             CCHHHHHHHHHHHHHHT-----TTCSCEEEEEEEEET-TEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHCCSSCC
T ss_pred             CCHHHHHHHHHHHHHHh-----cCcccEEEEEEEEeC-CCCEEEEECCCccEEecCeEEeccchHHHHHHHHHHhccCCC
Confidence            99999999999988764     379999999999998 489999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          185 REEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       185 ~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      ++||++++++||..+.++|..++++++|++|++++
T Consensus       177 ~eEA~~la~~al~~a~~rD~~sg~~iev~vI~kdg  211 (261)
T 3nzj_H          177 KEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEIGK  211 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCCSCEEEEEEETTS
T ss_pred             HHHHHHHHHHHHHHHHhhCCCCCCcEEEEEEECCC
Confidence            99999999999999999999999999999999987

>1ryp_M 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_M* 1jd2_L* 1g65_L 1vsy_M 1z7q_M 2f16_L* 2fak_L* 2fny_L* 2gpl_L* 3d29_L* 3dy3_L* 3dy4_L* 3e47_L* 3gpj_L* 3gpt_L* 3gpw_L* 3hye_L* 3l5q_Q 3mg0_L* 3mg4_L* ...

Probab=100.00  E-value=1.5e-43  Score=296.33  Aligned_cols=189  Identities=20%  Similarity=0.298  Sum_probs=179.9

Q ss_pred             HhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhC-CCC
Q 025640           27 AIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQ-EPM  105 (250)
Q Consensus        27 a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~-~~~  105 (250)
                      .+++|+|+|||+++||||||+|+|.++|+++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++ .++
T Consensus         5 ~v~~Gtt~vgi~~~dgVvlaaD~r~~~g~~i~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~   84 (222)
T 1ryp_M            5 YGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKL   84 (222)
T ss_dssp             CCCCCCEEEEEECSSCEEEEEECCEEETTEEEESCCCCCEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHTTTCCC
T ss_pred             cccCCccEEEEEeCCEEEEEEecccccCCEecCCCcCcEEEeCCCEEEEccccHHHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence            4689999999999999999999999999988888999999999999999999999999999999999999999999 999


Q ss_pred             CHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhh-------
Q 025640          106 PVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQD-------  178 (250)
Q Consensus       106 ~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~-------  178 (250)
                      +++.+++.+++.++.  +  +.+||++++||||||++++|+||.+||.|++.+++++|+|+|+.+++++||+.       
T Consensus        85 ~v~~la~~l~~~ly~--~--r~~P~~v~~ivaG~D~~g~p~Ly~~dp~G~~~~~~~~a~Gsg~~~a~~~Le~~~~~~~~~  160 (222)
T 1ryp_M           85 SINSAARNIQHLLYG--K--RFFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQY  160 (222)
T ss_dssp             CHHHHHHHHHHHHHT--T--TTSCCCEEEEEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTSCTTCB
T ss_pred             CHHHHHHHHHHHHHh--c--CCCCceEEEEEEEEcCCCCeEEEEECCCcCEEecCEEEEcCcHHHHHHHHhccccccccc
Confidence            999999999999864  3  26899999999999986679999999999999999999999999999999998       


Q ss_pred             ----------CCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          179 ----------YKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       179 ----------~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                                |+++||++||++++++||..+.+++..++++++|++|++++
T Consensus       161 ~~~~~~~~~~~~~~~s~eeA~~la~~al~~a~~rd~~sg~~i~v~vi~~~g  211 (222)
T 1ryp_M          161 EPGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDG  211 (222)
T ss_dssp             CTTSTTCSBCCCCCCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTE
T ss_pred             ccccccccccCCCCCCHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEcCCC
Confidence                      88999999999999999999999999999999999999987

>3unf_N Proteasome subunit beta type-9; antigen presentation, drug development, protein degradation, hydrolase-hydrolase inhibitor complex; HET: 04C; 2.90A {Mus musculus} PDB: 3unh_N

Probab=100.00  E-value=7.6e-44  Score=293.30  Aligned_cols=196  Identities=18%  Similarity=0.255  Sum_probs=182.9

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++.+++++.++
T Consensus         1 TT~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a   80 (199)
T 3unf_N            1 TTIMAVEFDGGVVVGSDSRVSAGTAVVNRVFDKLSPLHQRIFCALSGSAADAQAIADMAAYQLELHGLELEEPPLVLAAA   80 (199)
T ss_dssp             CEEEEEECSSCEEEEECCCEEETTEEEESSCCCEEEEETTEEEEECSCHHHHHHHHHHHHHHHHHHHHHTTSCCCHHHHH
T ss_pred             CeEEEEEeCCeEEEEECCcccCCceeEccccCceEEcCCCEEEEecccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            68999999999999999999999777778999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecc-eEEEEeCChHHHHHHHHhhCCCCCCHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW-KAAAIGANNQAAQSILKQDYKDDISREEAVQ  190 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~-~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~  190 (250)
                      +++++.++.+     .|||++++||||||+.++|+||.  |+|++.++ +++++|+|+++++++||+.|+++||++||++
T Consensus        81 ~~l~~~l~~~-----~~p~~v~~lvaG~D~~~~p~ly~--p~G~~~~~~~~~~~Gsgs~~a~~~Le~~~~~~ms~eea~~  153 (199)
T 3unf_N           81 NVVKNISYKY-----REDLLAHLIVAGWDQREGGQVYG--TMGGMLIRQPFTIGGSGSSYIYGYVDAAYKPGMTPEECRR  153 (199)
T ss_dssp             HHHHHHHHHT-----TTTCCCCEEEEEEETTTEEEEEE--CGGGCCEECSEEEEEGGGGGGHHHHHHHCCSSCCHHHHHH
T ss_pred             HHHHHHHHhc-----CCCceEEEEEEEEeCCCCcEEEE--ECCCceecCCEEEEccCHHHHHHHHHhhcCCCCCHHHHHH
Confidence            9999999875     36999999999999867899999  99997655 5666799999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 025640          191 LALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL  237 (250)
Q Consensus       191 l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~  237 (250)
                      ++++||..+.+++..++++++|++|++++   ..++.++++||+.++
T Consensus       154 la~~al~~~~~~d~~sg~~i~v~vi~~~g---~~~~~l~~~ei~~~~  197 (199)
T 3unf_N          154 FTTNAITLAMNRDGSSGGVIYLVTITAAG---VDHRVILGDELPKFY  197 (199)
T ss_dssp             HHHHHHHHHHHHCTTCCSCEEEEEECSSC---EEEEEECGGGSCCCC
T ss_pred             HHHHHHHHHHHhccccCCCeEEEEEcCCC---EEEEEcCcccCcccc
Confidence            99999999999999999999999999987   568999999997654

>1iru_K 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_J* 3une_J 3unf_J* 3unh_J

Probab=100.00  E-value=8.7e-43  Score=287.43  Aligned_cols=191  Identities=21%  Similarity=0.238  Sum_probs=176.3

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++++++++.++
T Consensus         2 tt~vgi~~~dgVvlaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a   81 (201)
T 1iru_K            2 EYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAA   81 (201)
T ss_dssp             CCEEEEECSSEEEEEEECCEEETTEEEESSCCCEEECSSSEEEEEEESTTHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             ceEEEEEeCCEEEEEEcCccccCcEEEccCcceEEEecCCEEEEeCcCHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            78999999999999999999998777777899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +++++.+....+  ..+||++++||||||++++|+||.+||.|++.+++++|+|+|+++++++||+.|+++||++||+++
T Consensus        82 ~~~~~~l~~~~~--~~~p~~~~~lvaG~D~~~gp~Ly~id~~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~~s~eea~~l  159 (201)
T 1iru_K           82 NFTRRNLADCLR--SRTPYHVNLLLAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVEL  159 (201)
T ss_dssp             HHHHHHHHHHHT--SSSCCCEEEEEEEEETTTEEEEEEECTTCCEEECSEEEESHHHHHHHHHHHHHCCTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHh--cCCCccEEEEEEEEeCCCCeEEEEECCCcCeEECCEEEECCcHHHHHHHHHhcccCCCCHHHHHHH
Confidence            998875521111  237999999999999866899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCS  229 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~  229 (250)
                      +++||+.+.+|+..++++++|++|+++|     ++.++
T Consensus       160 ~~~al~~a~~rd~~sg~~i~v~vi~~~g-----~~~~~  192 (201)
T 1iru_K          160 LRKCLEELQKRFILNLPTFSVRIIDKNG-----IHDLD  192 (201)
T ss_dssp             HHHHHHHHHHTBCBCCCCEEEEEEETTE-----EECCC
T ss_pred             HHHHHHHHHhhccccCCceEEEEEcCCC-----eEEee
Confidence            9999999999999999999999999987     55554

>1ryp_I 20S proteasome; multicatalytic proteinase, protein degradation, antigen processing, hydrolase, protease; 1.90A {Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1g0u_H* 1jd2_H* 1g65_H 1vsy_I 1z7q_I 2f16_H* 2fak_H* 2fny_H* 2gpl_H* 3d29_H* 3dy3_H* 3dy4_H* 3e47_H* 3gpj_H* 3gpt_H* 3gpw_H* 3hye_H* 3l5q_M 3mg0_H* 3mg4_H* ...

Probab=100.00  E-value=3.1e-42  Score=288.31  Aligned_cols=182  Identities=19%  Similarity=0.272  Sum_probs=175.4

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|+++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++++++++.++
T Consensus         1 TT~vgi~~~dgVvlaaD~r~t~g~~~~~~~~~KI~~i~d~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~~a   80 (222)
T 1ryp_I            1 TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSAL   80 (222)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEEcCCcccCCeeecCCcccEEEecCCEEEEecccHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            58999999999999999999999988888899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.++.+     .|||++++||||||+ .||+||.+||.|++.+++++|+|+|+.+++++||+.|+++||++||+++
T Consensus        81 ~~l~~~l~~~-----~~p~~v~~lvaG~D~-~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eeA~~l  154 (222)
T 1ryp_I           81 QMLKQHLFKY-----QGHIGAYLIVAGVDP-TGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKL  154 (222)
T ss_dssp             HHHHHHHHHT-----TTCSCEEEEEEEEET-TEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHCCSSCCHHHHHHH
T ss_pred             HHHHHHHhhc-----CCCCCeeEEEEEEeC-CCCEEEEECCCCCEEecCEEEECCCHHHHHHHHHhhCCCCcCHHHHHHH
Confidence            9999998865     479999999999998 5899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      +++||+.+.++|..++++++|++|++++
T Consensus       155 a~~al~~~~~~d~~sg~~i~v~vi~~~g  182 (222)
T 1ryp_I          155 ASDAIQAGIWNDLGSGSNVDVCVMEIGK  182 (222)
T ss_dssp             HHHHHHHHHHHCTTCCSCEEEEEEETTS
T ss_pred             HHHHHHHHHhccccCCCcEEEEEEECCC
Confidence            9999999999999999999999999886

>1iru_I 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 PDB: 3unb_H* 3une_H

Probab=100.00  E-value=6.3e-42  Score=288.49  Aligned_cols=189  Identities=18%  Similarity=0.275  Sum_probs=178.6

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.++|+++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++++++++.++
T Consensus         1 TTivgi~~~dgVVlaaD~r~t~g~~~~~~~~~KI~~i~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~~~~~~~v~~la   80 (234)
T 1iru_I            1 TTIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTAN   80 (234)
T ss_dssp             CCEEEEEETTEEEEEECCCEESSSBEEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHH
T ss_pred             CeEEEEEeCCEEEEEEcCCcccCceeccCcccceEEecCCEEEEecCcHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            58999999999999999999999998878899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.++.++     +||++++||||||+ .||+||.+||.|++.+++++|+|+|+++++++||+.|+++||++||+++
T Consensus        81 ~~l~~~l~~~~-----~~~~v~llvaG~D~-~gp~Ly~idp~G~~~~~~~~aiGsgs~~a~~~Le~~~~~~ms~eeA~~l  154 (234)
T 1iru_I           81 RMLKQMLFRYR-----GYIGAALVLGGVDV-TGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNL  154 (234)
T ss_dssp             HHHHHHHHHTT-----TCSCEEEEEEEECS-SCEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHSCCTTCCHHHHHTH
T ss_pred             HHHHHHHHhcC-----CCCceeEEEEEEcC-CCCEEEEECCCCCEEecCEEEECCchHHHHHHHHHhccCCCCHHHHHHH
Confidence            99999988763     59999999999998 5899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHH
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPE  231 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~  231 (250)
                      +++||..+.+++..++++++|++|++++     ++.+.+.
T Consensus       155 a~~al~~a~~~d~~sg~~i~v~vi~k~g-----~~~~~~~  189 (234)
T 1iru_I          155 VSEAIAAGIFNDLGSGSNIDLCVISKNK-----LDFLRPY  189 (234)
T ss_dssp             HHHHHHHHHHHCTTCCSCEEEEEEETTE-----EECCSEE
T ss_pred             HHHHHHHHHHhcccCCCCEEEEEEECCc-----EEEEcce
Confidence            9999999999999999999999999986     5555543

>2z3b_A ATP-dependent protease HSLV; N-terminal nucleophIle hydrolase; 2.50A {Bacillus subtilis} SCOP: d.153.1.4 PDB: 2z3a_A 1yyf_D* 3ty6_A

Probab=100.00  E-value=9.8e-36  Score=241.16  Aligned_cols=170  Identities=19%  Similarity=0.209  Sum_probs=151.9

Q ss_pred             cCCccEEEEEeCCEEEEEEEcccCCCcc-cccCCcCcEEEe-cCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCC
Q 025640           29 GNAGSAIGILSKDGVVLVGEKKVTSKLL-QTSTSTEKMYKI-DDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMP  106 (250)
Q Consensus        29 ~~g~t~igi~~~dgvvla~d~~~~~~~~-~~~~~~~Ki~~i-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~  106 (250)
                      .+|+|+|||+++||||||+|+|.++|.+ +.+++.+||++| +++++|+++|..+|++.+.+.++.++..|+   +    
T Consensus         3 ~~GtTivgi~~~dgVvlaaD~r~t~g~~~i~~~~~~KI~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~y~---g----   75 (180)
T 2z3b_A            3 FHATTIFAVQHKGRSAMSGDGQVTFGQAVVMKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEEYN---G----   75 (180)
T ss_dssp             BCCCCEEEEEETTEEEEEECCCEEETTTEEEESCCCCEEEETTTTEEEEECSCHHHHHHHHHHHHHHHHHTT---T----
T ss_pred             CCCeEEEEEEECCEEEEEECCCccCCCceEecCCCCcEEEECCCCEEEEeCchHHHHHHHHHHHHHHHHHhc---C----
Confidence            6799999999999999999999999876 777899999999 999999999999999999999999999876   2    


Q ss_pred             HHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceec--ceEEEEeCChHHHHHHHHhhCCC---
Q 025640          107 VEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGG--WKAAAIGANNQAAQSILKQDYKD---  181 (250)
Q Consensus       107 ~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~--~~~~a~G~g~~~~~~~L~~~~~~---  181 (250)
                        .+.+.++++.+.+++....|||++++||+  |   +|+||.+||.|++.+  ++++|+|+|+.+++++||+.|++   
T Consensus        76 --~~~~~~~~l~~~~~~~~~~rp~~~~~lva--d---~p~ly~~d~~G~~~~~~~~~~a~Gsgs~~a~~~le~~~~~~~~  148 (180)
T 2z3b_A           76 --NLKRAAVELAKEWRSDKVLRKLEAMLIVM--N---QDTLLLVSGTGEVIEPDDGILAIGSGGNYALAAGRALKKHAGE  148 (180)
T ss_dssp             --CHHHHHHHHHHHHHHCTTGGGCCCCEEEE--C---SSCEEEECTTCCEECCSSSEEEESTTHHHHHHHHHHHHHHHGG
T ss_pred             --ChHHHHHHHHHHHHhhhCcCcceEEEEEE--c---CCeEEEECCCCcEEEeCCCEEEECCCHHHHHHHHHHhhhccCC
Confidence              23333344445556667789999999999  3   699999999999997  59999999999999999999998   


Q ss_pred             CCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       182 ~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      +|+.+|   ++.+||+.+.+||..++++++|.+|
T Consensus       149 ~mt~ee---l~~~al~~a~~rd~~sg~~i~v~~i  179 (180)
T 2z3b_A          149 SMSASE---IARAALETAGEICVYTNDQIILEEL  179 (180)
T ss_dssp             GCCHHH---HHHHHHHHHHHHCTTCCSCCEEEEE
T ss_pred             CCCHHH---HHHHHHHHHHHhcCccCCeEEEEEE
Confidence            999999   4789999999999999999999988

>1m4y_A ATP-dependent protease HSLV; N-terminal catalytic threonine residue, hydrolase; 2.10A {Thermotoga maritima} SCOP: d.153.1.4

Probab=100.00  E-value=4.2e-35  Score=235.58  Aligned_cols=167  Identities=19%  Similarity=0.216  Sum_probs=147.4

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEe-cCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKI-DDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQL  110 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l  110 (250)
                      +|+|||+++||||||+|+|.++|.++.+++.+||++| +++++++++|..+|++.+.+.++.++..|+..     .++.+
T Consensus         1 tt~vgi~~~dgVvlaaD~r~~~g~~i~~~~~~Ki~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~~-----~~~~~   75 (171)
T 1m4y_A            1 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREWGGN-----LTKAA   75 (171)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTTC-----HHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCCEEEeCCcceEEEeCCCCEEEEeCccHHHHHHHHHHHHHHHHHhccc-----HHHHH
Confidence            5899999999999999999999877777889999999 99999999999999999999999999987633     24444


Q ss_pred             HHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce--EEEEeCChHHHHHHHHhhCC-CCCCHHH
Q 025640          111 VQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK--AAAIGANNQAAQSILKQDYK-DDISREE  187 (250)
Q Consensus       111 a~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~--~~a~G~g~~~~~~~L~~~~~-~~~s~~e  187 (250)
                      ++.    .+.++++.+.|||++++|++  |   +|+||.+||.|++.+++  ++|+|+|+++++++||+.|+ ++||.  
T Consensus        76 ~~l----~~~~~~~~~~~~~~~~~lv~--D---~p~Ly~~d~~G~~~~~~~~~~a~Gsgs~~a~~~le~~~~~~~ms~--  144 (171)
T 1m4y_A           76 VEL----AKDWRTDRVLRRLEALLLVA--D---KENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLSA--  144 (171)
T ss_dssp             HHH----HHHHHHCTTGGGCCCEEEEE--C---SSCEEEECTTSCEECCSSSEEEESTTHHHHHHHHHHHHHHCCCCH--
T ss_pred             HHH----HHHHHHhCCCCceEEEEEEE--c---CCEEEEECCCCCEEecCCCEEEECCcHHHHHHHHHHhcccCCCCH--
Confidence            443    33445555678999999988  4   79999999999999987  99999999999999999999 99996  


Q ss_pred             HHHHHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          188 AVQLALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       188 a~~l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                       ++++++||+.+.+||..++++++|.++
T Consensus       145 -~~l~~~al~~a~~rd~~sg~~i~v~~~  171 (171)
T 1m4y_A          145 -REIVEKAMTIAGEICIYTNQNIVIEEV  171 (171)
T ss_dssp             -HHHHHHHHHHHHHHCTTCCSCCEEEEC
T ss_pred             -HHHHHHHHHHHHHhCcccCCeEEEEEC
Confidence             678999999999999999999999864

>1g3k_A ATP-dependent protease HSLV; hydrolase; 1.90A {Haemophilus influenzae} SCOP: d.153.1.4 PDB: 1g3i_G 1jjw_A 1kyi_G* 1ofh_G* 1ofi_G* 1e94_A* 1g4a_B* 1g4b_M 1hqy_A* 1ht1_C* 1ht2_A* 1ned_A

Probab=100.00  E-value=8.4e-35  Score=234.46  Aligned_cols=168  Identities=16%  Similarity=0.154  Sum_probs=147.6

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEe-cCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKI-DDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQL  110 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i-~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l  110 (250)
                      +|+|||+++||||||+|+|.++|.++.+++.+||++| ++|++++++|..+|++.+.+.++.++..|+.      +.   
T Consensus         1 tT~vgi~~~dgVvlaaD~r~t~g~~i~~~~~~Ki~~i~~~~i~~~~aG~~aD~~~l~~~~~~~~~~~~~------~~---   71 (174)
T 1g3k_A            1 TTIVSVRRNGQVVVGGDGQVSLGNTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFELFERKLEMHQG------HL---   71 (174)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHTTT------CH---
T ss_pred             CeEEEEEECCEEEEEECCCCccCCeeEeCCCCcEEEECCCCEEEEeCccHHHHHHHHHHHHHHHHHhcC------cH---
Confidence            5899999999999999999999977777899999999 9999999999999999999999999998764      33   


Q ss_pred             HHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce---EEEEeCChHHHHHHHHhhCC-CCCCHH
Q 025640          111 VQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK---AAAIGANNQAAQSILKQDYK-DDISRE  186 (250)
Q Consensus       111 a~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~---~~a~G~g~~~~~~~L~~~~~-~~~s~~  186 (250)
                      .+.++.+.+.++++.+.||+  .++++|+|   +|+||.+||+|++.+++   ++|+|+|+++++++||+.|+ ++|+.+
T Consensus        72 ~~~~~~l~~~~~~~~~~r~~--~~~l~g~d---~p~Ly~~d~~G~~~~~~~~~~~a~Gsgs~~a~~~le~~~~~~~mt~~  146 (174)
T 1g3k_A           72 LKSAVELAKDWRTDRALRKL--EAMLIVAD---EKESLIITGIGDVVQPEEDQILAIGSGGNYALSAARALVENTELSAH  146 (174)
T ss_dssp             HHHHHHHHHHHHHSTTGGGC--CCEEEEEC---SSCEEEEETTTEEECCCTTCEEEESTTHHHHHHHHHHHHHHCCCCHH
T ss_pred             HHHHHHHHHHHHhccCcCcc--eEEEEEEC---CCEEEEEcCCCcEEecCCCcEEEEcccHHHHHHHHHHhcccCCCCHH
Confidence            33344444445566567775  46777886   69999999999999988   99999999999999999999 999954


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCcEEEEEEE
Q 025640          187 EAVQLALKVLSKTMDSTSLTSDKLELAEVF  216 (250)
Q Consensus       187 ea~~l~~~~l~~~~~~~~~~~~~iei~ii~  216 (250)
                         +++.+||+.+.+||..++++++|++|+
T Consensus       147 ---~l~~~al~~a~~rd~~sg~~i~v~~i~  173 (174)
T 1g3k_A          147 ---EIVEKSLRIAGDICVFTNTNFTIEELP  173 (174)
T ss_dssp             ---HHHHHHHHHHHHHCTTCCSCCEEEEEC
T ss_pred             ---HHHHHHHHHHHHhccccCCceEEEEec
Confidence               799999999999999999999999985

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	250
d1rypc_	244	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	7e-85
d1iruc_	250	d.153.1.4 (C:) Proteasome alpha subunit (non-catal	1e-81
d1irug_	245	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	1e-79
d1rypg_	244	d.153.1.4 (G:) Proteasome alpha subunit (non-catal	3e-76
d1irua_	244	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	4e-73
d1rypb_	250	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	4e-72
d1rypf_	233	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	2e-71
d1irue_	234	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	2e-71
d1iruf_	238	d.153.1.4 (F:) Proteasome alpha subunit (non-catal	3e-70
d1irud_	243	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	2e-69
d1rypd_	241	d.153.1.4 (D:) Proteasome alpha subunit (non-catal	3e-69
d1rype_	242	d.153.1.4 (E:) Proteasome alpha subunit (non-catal	8e-68
d1rypa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	3e-67
d1yara1	221	d.153.1.4 (A:13-233) Proteasome alpha subunit (non	4e-67
d1j2pa_	243	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	4e-66
d1irub_	233	d.153.1.4 (B:) Proteasome alpha subunit (non-catal	1e-63
d1q5qa_	227	d.153.1.4 (A:) Proteasome alpha subunit (non-catal	3e-53
d1iruh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	3e-44
d1ryp1_	222	d.153.1.4 (1:) Proteasome beta subunit (catalytic)	1e-41
d1ryp2_	233	d.153.1.4 (2:) Proteasome beta subunit (catalytic)	7e-40
d1yarh1	203	d.153.1.4 (H:1-203) Proteasome beta subunit (catal	8e-40
d1j2qh_	202	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	9e-40
d1rypi_	222	d.153.1.4 (I:) Proteasome beta subunit (catalytic)	1e-39
d1irui_	220	d.153.1.4 (I:) Proteasome beta subunit (catalytic)	2e-39
d1irul_	201	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	5e-39
d1rypl_	212	d.153.1.4 (L:) Proteasome beta subunit (catalytic)	7e-39
d1rypk_	198	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	3e-37
d1iruk_	199	d.153.1.4 (K:) Proteasome beta subunit (catalytic)	2e-36
d1iru2_	217	d.153.1.4 (2:) Proteasome beta subunit (catalytic)	1e-35
d1ryph_	205	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	2e-35
d1iruj_	204	d.153.1.4 (J:) Proteasome beta subunit (catalytic)	3e-35
d1q5qh_	224	d.153.1.4 (H:) Proteasome beta subunit (catalytic)	6e-34
d1rypj_	204	d.153.1.4 (J:) Proteasome beta subunit (catalytic)	1e-33
d1iru1_	213	d.153.1.4 (1:) Proteasome beta subunit (catalytic)	4e-30
d1m4ya_	171	d.153.1.4 (A:) HslV (ClpQ) protease {Thermotoga ma	1e-09
d2z3ba1	180	d.153.1.4 (A:1-180) HslV (ClpQ) protease {Bacillus	1e-09
d1g3ka_	173	d.153.1.4 (A:) HslV (ClpQ) protease {Haemophilus i	4e-08

>d1rypc_ d.153.1.4 (C:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 244

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  251 bits (641), Expect = 7e-85
 Identities = 147/243 (60%), Positives = 191/243 (78%), Gaps = 1/243 (0%)

Query: 2   SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
           SRRYDSRTTIFSPEGRLYQVEYA+E+I +AG+AIGI++ DG+VL  E+KVTS LL+  TS
Sbjct: 2   SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTS 61

Query: 62  TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
           TEK+YK++D +A AVAG+ +DA ILINTAR+ AQ Y   Y E +PVE LV+ L D KQGY
Sbjct: 62  TEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGY 121

Query: 122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD 181
           TQ GGLRPFGVSF++AG+D  YG+QLY S+PSGNY GWKA ++GAN  AAQ++L+ DYKD
Sbjct: 122 TQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKD 181

Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLM-PSGKVKYQVCSPEALSKLLVKH 240
           D+  ++A++LALK LSKT DS++LT D+LE A +      G+V  ++  P+ +  +LVK 
Sbjct: 182 DMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKT 241

Query: 241 GVT 243
           G+T
Sbjct: 242 GIT 244

>d1iruc_ d.153.1.4 (C:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 250

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  243 bits (620), Expect = 1e-81
 Identities = 144/248 (58%), Positives = 187/248 (75%), Gaps = 2/248 (0%)

Query: 2   SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
           SRRYDSRTTIFSPEGRLYQVEYAMEAIG+AG+ +GIL+ DGV+L  E++   KLL     
Sbjct: 1   SRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFF 60

Query: 62  TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
           +EK+YK+++ +AC+VAGI SDAN+L N  R+ AQRY   YQEP+P EQLV +LCD KQ Y
Sbjct: 61  SEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAY 120

Query: 122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDY-K 180
           TQFGG RPFGVS L+ GWDK+YGFQLY SDPSGNYGGWKA  IG N+ AA S+LKQDY +
Sbjct: 121 TQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKE 180

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH 240
            +++ + A+ LA+KVL+KTMD + L+++K+E+A      +GK   +V   + + +L+ KH
Sbjct: 181 GEMTLKSALALAIKVLNKTMDVSKLSAEKVEIA-TLTRENGKTVIRVLKQKEVEQLIKKH 239

Query: 241 GVTQPAAE 248
              +  AE
Sbjct: 240 EEEEAKAE 247

>d1irug_ d.153.1.4 (G:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 245

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  237 bits (606), Expect = 1e-79
 Identities = 81/239 (33%), Positives = 133/239 (55%), Gaps = 4/239 (1%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           +   YD   + FSP+GR++QVEYAM+A+ N+ +AIGI  KDGVV   EK V SKL     
Sbjct: 3   IGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLY-EEG 61

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
           S ++++ +D HV  AVAG+++DA  L + AR +A  +   +   +P++ L   +      
Sbjct: 62  SNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHA 121

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YT +  +RPFG SF+   +  N G QLYM DPSG   G+   AIG   QAA++ +++   
Sbjct: 122 YTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQM 181

Query: 181 DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
            +++  + V+   K++    D     + +LEL+ V  + +G+ +     P+ + +   K
Sbjct: 182 KEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEI---VPKDIREEAEK 237

>d1rypg_ d.153.1.4 (G:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 244

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  229 bits (584), Expect = 3e-76
 Identities = 81/236 (34%), Positives = 132/236 (55%), Gaps = 6/236 (2%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   ++FSP+GR +QVEYA++A+ N  ++IGI   DGVV   EK +TSKLL    +  K
Sbjct: 4   YDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKN-VK 62

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +D H+ C  +G++ D   L+N  R +A  +   Y+ P+P+      L    Q +T +
Sbjct: 63  IQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLY 122

Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQ---DYKD 181
             +RPFGVS +F G DKN G  LYM +PSG+Y G+K AA G   Q+A++ L++    + +
Sbjct: 123 NSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPE 181

Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            +S  EAV+ A K++    +       +LE++   L  +    ++    + L + +
Sbjct: 182 GLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNG-LHKFVKGDLLQEAI 236

>d1irua_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 244

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  221 bits (563), Expect = 4e-73
 Identities = 79/241 (32%), Positives = 128/241 (53%), Gaps = 8/241 (3%)

Query: 2   SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAG-SAIGILSKDGVVLVGEKKVTSKLLQTST 60
           S  +D   TIFSPEGRLYQVEYA +AI   G +++ +  KD  V+V +KKV  KLL +ST
Sbjct: 5   SAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSST 64

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQG 120
               ++KI +++ C + G+ +D+   +  AR +A  + Y Y   +PV+ L + + D  Q 
Sbjct: 65  V-THLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQV 123

Query: 121 YTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK 180
           YTQ   +RP G   +  G D+  G Q+Y  DP+G Y G+KA A G     + S L++  K
Sbjct: 124 YTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVK 183

Query: 181 DD--ISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLV 238
                + E+ V+ A+  LS  +        ++E+    ++     K+++ +   +   LV
Sbjct: 184 KKFDWTFEQTVETAITCLSTVLS-IDFKPSEIEVG---VVTVENPKFRILTEAEIDAHLV 239

Query: 239 K 239
            
Sbjct: 240 A 240

>d1rypb_ d.153.1.4 (B:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 250

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  218 bits (557), Expect = 4e-72
 Identities = 79/216 (36%), Positives = 124/216 (57%), Gaps = 3/216 (1%)

Query: 1   MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTST 60
           M+ RY    T FSP G+L Q++YA+ A+    +++GI + +GVV+  EKK +S L   S 
Sbjct: 1   MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAM-SE 59

Query: 61  STEKMYKIDDHVACAVAGIMSDANILINTARVQAQ-RYTYAYQEPMPVEQLVQSLCDTKQ 119
           +  K+  +   +    +G+  D  +L++ +R  A   Y   Y E  P + LV  +    Q
Sbjct: 60  TLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQ 119

Query: 120 GYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDY 179
             TQ GG+RPFGVS L AG D+  GF LY  DPSG+Y  WKA AIG  + AA++ L++ +
Sbjct: 120 EATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRW 179

Query: 180 KDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEV 215
            D++  E+A+ +AL  L ++++      D +ELA +
Sbjct: 180 NDELELEDAIHIALLTLKESVE-GEFNGDTIELAII 214

>d1rypf_ d.153.1.4 (F:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 233

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  216 bits (552), Expect = 2e-71
 Identities = 79/238 (33%), Positives = 121/238 (50%), Gaps = 12/238 (5%)

Query: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
            YD  T  FSP GRL+QVEYA+EAI      +G+ S    VLV  K+   +L   S+  +
Sbjct: 4   NYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADEL---SSYQK 60

Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
           K+ K D+H+  ++AG+  DA +L N  R Q    +  +   + VE+    LCD  Q  TQ
Sbjct: 61  KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQ 120

Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDI 183
             G RP+GV  L  G+D   G  L    PSGN       AIGA +Q A++ L++     I
Sbjct: 121 SYGGRPYGVGLLIIGYD-KSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI 179

Query: 184 ----SREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
               + +E ++  ++ +S+++   SLT D L +A V         + +   EA++K +
Sbjct: 180 KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIV----GKDTPFTIYDGEAVAKYI 233

>d1irue_ d.153.1.4 (E:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 234

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  216 bits (551), Expect = 2e-71
 Identities = 89/238 (37%), Positives = 142/238 (59%), Gaps = 12/238 (5%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD     FSPEGRL+QVEY +EAI    +AIGI + +GV L  EK++TS L++ S S EK
Sbjct: 1   YDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPS-SIEK 59

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + +ID H+ CA++G+++DA  LI+ ARV+ Q + + Y E M VE + Q++ +    + + 
Sbjct: 60  IVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEE 119

Query: 125 GG-----LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDY 179
                   RPFGV+ LF G D+  G QL+  DPSG +    A AIG+ ++ AQS L++ Y
Sbjct: 120 DADPGAMSRPFGVALLFGGVDEK-GPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQELY 178

Query: 180 KDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
              ++ +EA++ +L +L + M+   L +  +ELA V         + + + E L +++
Sbjct: 179 HKSMTLKEAIKSSLIILKQVMEE-KLNATNIELATV----QPGQNFHMFTKEELEEVI 231

>d1iruf_ d.153.1.4 (F:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 238

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  213 bits (544), Expect = 3e-70
 Identities = 72/239 (30%), Positives = 133/239 (55%), Gaps = 11/239 (4%)

Query: 4   RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
           +YD+  T++SP+GR++Q+EYAMEA+    + +G+ SK   VLV  K+  S+L   +   +
Sbjct: 2   QYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSEL---AAHQK 58

Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
           K+  +D+H+  ++AG+ +DA +L N  R +     + +  P+PV +LV  +    Q  TQ
Sbjct: 59  KILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQ 118

Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD-- 181
             G RP+GV  L AG+D   G  ++ + PS NY   +A +IGA +Q+A++ L++   +  
Sbjct: 119 RYGRRPYGVGLLIAGYDDM-GPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM 177

Query: 182 DISREEAVQLALKVLSKTMDS-TSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
           + +  E V+  L+ L +T+ +   LT+  + +  V       +++ +   + +S  L  
Sbjct: 178 ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIV----GKDLEFTIYDDDDVSPFLEG 232

>d1irud_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 243

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  211 bits (538), Expect = 2e-69
 Identities = 85/237 (35%), Positives = 136/237 (57%), Gaps = 10/237 (4%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+G L+QVEYA EA+    +A+G+  +D VVL  EKK  +KL     +  K
Sbjct: 2   YDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQ-DERTVRK 60

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +  +DD+V  A AG+ +DA I+IN ARV+ Q +    ++P+ VE + + +   KQ YTQ 
Sbjct: 61  ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQS 120

Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDD-- 182
            G RPFG+S L  G+D +   +LY +DPSG Y  WKA AIG   ++ +  L+++Y D+  
Sbjct: 121 NGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAI 180

Query: 183 ISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
            + +  ++L +K L + + S       +ELA +          ++ +PE + K + +
Sbjct: 181 ETDDLTIKLVIKALLEVVQS---GGKNIELAVM----RRDQSLKILNPEEIEKYVAE 230

>d1rypd_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 241

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  211 bits (537), Expect = 3e-69
 Identities = 83/239 (34%), Positives = 134/239 (56%), Gaps = 11/239 (4%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   +IFSP+G ++QVEYA+EA+     A+G+  K+ VVL  E++ T KL  T  +  K
Sbjct: 2   YDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSK 61

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           + KID HV  + +G+ +D+ ILI  ARV+AQ +    ++P+ VE L + +   +Q YTQ 
Sbjct: 62  VSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQS 121

Query: 125 GGLRPFGVSFLFAGWDKNY-GFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD-- 181
           GG+RPFGVS L AG+D      +LY ++PSG Y  W A  IG N++  +  L+++Y    
Sbjct: 122 GGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKE 181

Query: 182 -DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
              + EE V+L ++ L + +      +  +E+  V             S E +++ + +
Sbjct: 182 PPATVEECVKLTVRSLLEVVQ---TGAKNIEITVV----KPDSDIVALSSEEINQYVTQ 233

>d1rype_ d.153.1.4 (E:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 242

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  207 bits (528), Expect = 8e-68
 Identities = 86/240 (35%), Positives = 143/240 (59%), Gaps = 12/240 (5%)

Query: 6   DSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKM 65
           D   + FSPEGRL+QVEY++EAI    +AIGI +K+GVVL  EK+ TS LL++ +  EK+
Sbjct: 1   DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDS-IEKI 59

Query: 66  YKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFG 125
            +ID H+ CA++G+ +DA  +I  AR  A  +   Y E + VE L QS+CD    + +  
Sbjct: 60  VEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGA 119

Query: 126 G------LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDY 179
                   RPFGV+ L AG D + G+QL+ ++PSG +  + A AIG+ ++ AQ+ L  ++
Sbjct: 120 SGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEW 179

Query: 180 KDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
              ++ +EA  L LK+L + M+   L  +  +L+ +    + +  +++   E  ++L+ +
Sbjct: 180 HSSLTLKEAELLVLKILKQVMEE-KLDENNAQLSCI----TKQDGFKIYDNEKTAELIKE 234

>d1rypa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 243

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  206 bits (524), Expect = 3e-67
 Identities = 77/243 (31%), Positives = 116/243 (47%), Gaps = 15/243 (6%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGS-AIGILSKDGVVLVGEKKVTSKLLQTSTSTE 63
           YD   TIFSPEGRLYQVEYA +A       ++ +  KD  V++ +KKV  KLL   T+  
Sbjct: 3   YDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLD-PTTVS 61

Query: 64  KMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQ 123
            ++ I   +   V G + DA      A+ +A  + Y Y   MP + L + + +  Q YTQ
Sbjct: 62  YIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQ 121

Query: 124 FGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDI 183
              +RP GV   F   D+  G  +Y +DP+G Y G+KA A G   Q   + L+  +K   
Sbjct: 122 RAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSK 181

Query: 184 -------SREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKL 236
                  S E+ V+ A+  +   +  T  + + LE+         K K+   S E + + 
Sbjct: 182 IDHINEESWEKVVEFAITHMIDALG-TEFSKNDLEVGVA-----TKDKFFTLSAENIEER 235

Query: 237 LVK 239
           LV 
Sbjct: 236 LVA 238

>d1yara1 d.153.1.4 (A:13-233) Proteasome alpha subunit (non-catalytic) {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Length = 221

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

 Score =  204 bits (521), Expect = 4e-67
 Identities = 88/228 (38%), Positives = 143/228 (62%), Gaps = 7/228 (3%)

Query: 10  TIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKID 69
           T+FSP+GRL+QVEYA EA+    +A+G+   +GV+L+ +KKV S+L+    S EK+  ID
Sbjct: 1   TVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLI-EQNSIEKIQLID 59

Query: 70  DHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRP 129
           D+VA   +G+++DA +L++ AR+ AQ+    Y   + +E LV+ + D  Q YTQ+GG+RP
Sbjct: 60  DYVAAVTSGLVADARVLVDFARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRP 119

Query: 130 FGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAV 189
           +GVS +FAG D+  G +L+  DP+G    +KA AIG+   A  S L+++YK+++  +EAV
Sbjct: 120 YGVSLIFAGIDQI-GPRLFDCDPAGTINEYKATAIGSGKDAVVSFLEREYKENLPEKEAV 178

Query: 190 QLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            L +K L  +++         E+A +    +   KY++   E + K L
Sbjct: 179 TLGIKALKSSLEE-GEELKAPEIASI----TVGNKYRIYDQEEVKKFL 221

>d1j2pa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 243

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score =  203 bits (517), Expect = 4e-66
 Identities = 94/235 (40%), Positives = 149/235 (63%), Gaps = 7/235 (2%)

Query: 5   YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEK 64
           YD   T+FSP+GRL+QVEYA EA+    +AIGI  K+GV+L+ +K+V SKLL    + EK
Sbjct: 5   YDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLL-EKDTIEK 63

Query: 65  MYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQF 124
           +YKID+H+  A +G+++DA +LI+ AR++AQ     Y  P+ V++L + +CD KQ YTQ+
Sbjct: 64  IYKIDEHICAATSGLVADARVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQY 123

Query: 125 GGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDIS 184
           GG+RPFGVS L AG ++    +LY +DPSG    +KA AIG    A     +++Y+DD+S
Sbjct: 124 GGVRPFGVSLLIAGVNEVP--KLYETDPSGALLEYKATAIGMGRMAVTEFFEKEYRDDLS 181

Query: 185 REEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
            ++A+ L L  +  +++ + L  + +E+     +      ++  SPE L   + +
Sbjct: 182 FDDAMVLGLVAMGLSIE-SELVPENIEVG---YVKVDDRTFKEVSPEELKPYVER 232

>d1irub_ d.153.1.4 (B:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 233

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  196 bits (500), Expect = 1e-63
 Identities = 85/238 (35%), Positives = 128/238 (53%), Gaps = 8/238 (3%)

Query: 2   SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTS 61
            R Y    T FSP G+L Q+EYA+ A+     ++GI + +GVVL  EKK  S L     S
Sbjct: 2   ERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILY-DERS 60

Query: 62  TEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGY 121
             K+  I  H+    +G+  D  +L++ AR  AQ+Y   YQEP+P  QLVQ +    Q Y
Sbjct: 61  VHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEY 120

Query: 122 TQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD 181
           TQ GG+RPFGVS L  GW++     L+ SDPSG Y  WKA A+G N    ++ L++ Y +
Sbjct: 121 TQSGGVRPFGVSLLICGWNEGRP-YLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE 179

Query: 182 DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
           D+  E+A+  A+  L ++ +   +T D +E+         +  ++  +P  +   L  
Sbjct: 180 DLELEDAIHTAILTLKESFE-GQMTEDNIEVGIC-----NEAGFRRLTPTEVKDYLAA 231

>d1q5qa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Rhodococcus erythropolis [TaxId: 1833]} Length = 227

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

 Score =  169 bits (430), Expect = 3e-53
 Identities = 43/227 (18%), Positives = 83/227 (36%), Gaps = 19/227 (8%)

Query: 20  QVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGI 79
           + E A + I    S + +  +DGV+ V E          ST+  K+ ++ D +  A  G 
Sbjct: 8   RSELARKGIARGRSVVVLTFRDGVLFVAENP--------STALHKVSELYDRLGFAAVGK 59

Query: 80  MSDANILINTARVQAQRYTYAYQE-PMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAG 138
            ++   L     V A    Y+Y    +    L  +   T          +P+ V    A 
Sbjct: 60  YNEFENLRRAGIVHADMRGYSYDRRDVTGRSLANAYAQTLG-TIFTEQPKPYEVEICVAE 118

Query: 139 WDKNY---GFQLYMSDPSGNYGGWKAAAIGA-NNQAAQSILKQDYKDDISREEAVQLALK 194
             +       QLY     G+    +   +     +   + +++ Y+ D+  E AV +A+ 
Sbjct: 119 VGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATAMRESYRADLDLEAAVGIAVN 178

Query: 195 VLSKTMDSTS----LTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL 237
            L +          +    LE+A V      +  ++  +  AL +L+
Sbjct: 179 ALRQGGAGEGEKRNVDVASLEVA-VLDQSRPRRAFRRIAGTALEQLV 224

>d1iruh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 202

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  145 bits (367), Expect = 3e-44
 Identities = 40/206 (19%), Positives = 77/206 (37%), Gaps = 8/206 (3%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + + +    GVVL  + + T+     +  T+K+  I D + C  +G  +D   + +    
Sbjct: 2   TIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTY 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           Q   ++    EP  V        +    Y +           + AGWD   G Q+Y    
Sbjct: 62  QLGFHSIELNEPPLVHTAASLFKEMCYRYRED-----LMAGIIIAGWDPQEGGQVYSVPM 116

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLEL 212
            G       A  G+ +      +   Y++ +++EE +Q     L+  M+    +   + L
Sbjct: 117 GGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVIRL 176

Query: 213 AEVFLMPSGKVKYQVCSPEALSKLLV 238
           A +       V+ QV   + + K  V
Sbjct: 177 AAI---AESGVERQVLLGDQIPKFAV 199

>d1ryp1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 222

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  139 bits (352), Expect = 1e-41
 Identities = 38/201 (18%), Positives = 71/201 (35%), Gaps = 20/201 (9%)

Query: 30  NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINT 89
           N G+ +GI  +D  VL G+ +  +     S    K++   D++  +  G  +D + L+  
Sbjct: 8   NGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKR 67

Query: 90  ARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYM 149
            +   + Y + + +       + S     Q         P+ V  + AG D++    +Y 
Sbjct: 68  FKNSVKWYHFDHNDKKLS---INSAARNIQHLLYGKRFFPYYVHTIIAGLDEDGKGAVYS 124

Query: 150 SDPSGNYGGWKAAAIGANNQAAQSILKQDYK-----------------DDISREEAVQLA 192
            DP G+Y   +  A GA        L                        +S EE ++L 
Sbjct: 125 FDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKLV 184

Query: 193 LKVLSKTMDSTSLTSDKLELA 213
               +   +      D LE+ 
Sbjct: 185 RDSFTSATERHIQVGDGLEIL 205

>d1ryp2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 233

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  135 bits (341), Expect = 7e-40
 Identities = 30/199 (15%), Positives = 62/199 (31%), Gaps = 8/199 (4%)

Query: 25  MEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDAN 84
            + I    S I +   +GV++  +   +   L      E++  + D+    ++G +SD  
Sbjct: 2   QQPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQ 61

Query: 85  ILINTARVQAQRYTYAYQEPMPVEQLVQSLCD---TKQGYTQFGGLRPFGVSFLFAGWDK 141
            +    +       Y        E L  S          Y +   + P   + + AG   
Sbjct: 62  HIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQS 121

Query: 142 NYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD-----DISREEAVQLALKVL 196
           N    L   +  G        A G     A  +L++           + + A +  +  +
Sbjct: 122 NGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAM 181

Query: 197 SKTMDSTSLTSDKLELAEV 215
                  + +S    LA +
Sbjct: 182 RVLYYRDARSSRNFSLAII 200

>d1yarh1 d.153.1.4 (H:1-203) Proteasome beta subunit (catalytic) {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Length = 203

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

 Score =  134 bits (338), Expect = 8e-40
 Identities = 42/210 (20%), Positives = 93/210 (44%), Gaps = 10/210 (4%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +GI  KD V++  E++VT +      + +K+++ID +    +AG++ DA +L+   + 
Sbjct: 2   TTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKA 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           + + Y    +  MP+E +   L +            P+ V  L  G D      ++  D 
Sbjct: 62  ELELYRLQRRVNMPIEAVATLLSNMLNQVKYM----PYMVQLLVGGIDT--APHVFSIDA 115

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLEL 212
           +G       A+ G+ +     +L+  Y + ++ +E V L ++ +S      S +   +++
Sbjct: 116 AGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDLVIRAISAAKQRDSASGGMIDV 175

Query: 213 AEVFLMPSGKVKYQVCSPEALSKLLVKHGV 242
           A +    + K  Y     + +   + K G+
Sbjct: 176 AVI----TRKDGYVQLPTDQIESRIRKLGL 201

>d1j2qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score =  134 bits (338), Expect = 9e-40
 Identities = 52/208 (25%), Positives = 95/208 (45%), Gaps = 11/208 (5%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +G++ KDGVV+  EK+ T      S + +K+Y+I D +A   AG + DA  L    ++
Sbjct: 2   TTVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKI 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           +A  Y    +    V  +     +    Y       P+ V  L  G D   G  +Y  DP
Sbjct: 62  EANLYEIRRERKPTVRAIATLTSNLLNSYRY----FPYLVQLLIGGIDSE-GKSIYSIDP 116

Query: 153 SGN-YGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLE 211
            G         A G+ +  A  +L+  +  +I  +EAV+LA++ +   M   S + D ++
Sbjct: 117 IGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVELAVRAIYSAMKRDSASGDGID 176

Query: 212 LAEVFLMPSGKVKYQVCSPEALSKLLVK 239
           + ++      + ++   SPE + ++L K
Sbjct: 177 VVKI-----TEDEFYQYSPEEVEQILAK 199

>d1rypi_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 222

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  134 bits (339), Expect = 1e-39
 Identities = 34/181 (18%), Positives = 76/181 (41%), Gaps = 6/181 (3%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +G+   +GVV+  + + T   +    +  K+++I   + CA AG  +D   +      
Sbjct: 2   TIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGS 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
             + ++        V   +Q L      Y         G   + AG D   G  L+    
Sbjct: 62  NIELHSLYTSREPRVVSALQMLKQHLFKYQGH-----IGAYLIVAGVDPT-GSHLFSIHA 115

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLEL 212
            G+       ++G+ + AA ++L+  +K D+++EEA++LA   +   + +   +   +++
Sbjct: 116 HGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDV 175

Query: 213 A 213
            
Sbjct: 176 C 176

>d1irui_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 220

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  134 bits (337), Expect = 2e-39
 Identities = 33/183 (18%), Positives = 75/183 (40%), Gaps = 6/183 (3%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           +  G++ KDG+VL  + + T  ++    +  K++ I  ++ C  AG  +D ++       
Sbjct: 2   TIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISS 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
             + ++ +      V    + L      Y         G + +  G D   G  LY   P
Sbjct: 62  NLELHSLSTGRLPRVVTANRMLKQMLFRYR-----GYIGAALVLGGVDVT-GPHLYSIYP 115

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLEL 212
            G+        +G+ + AA ++ +  ++ D+  EEA  L  + ++  + +   +   ++L
Sbjct: 116 HGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDL 175

Query: 213 AEV 215
             +
Sbjct: 176 CVI 178

>d1irul_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 201

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  132 bits (333), Expect = 5e-39
 Identities = 37/205 (18%), Positives = 82/205 (40%), Gaps = 10/205 (4%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +    + GV++  + + T+     S + +K+ +I+ ++   +AG  +D +        
Sbjct: 2   TTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLAR 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           Q + Y    +E + V    + L +    Y          +  +  GWDK  G  LY  D 
Sbjct: 62  QCRIYELRNKERISVAAASKLLANMVYQYKGM----GLSMGTMICGWDKR-GPGLYYVDS 116

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLEL 212
            GN       ++G+ +  A  ++ + Y  D+  E+A  LA + + +     + +   + L
Sbjct: 117 EGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNL 176

Query: 213 AEVFLMPSGKVKYQVCSPEALSKLL 237
             V      +  +   S + ++ L 
Sbjct: 177 YHV-----REDGWIRVSSDNVADLH 196

>d1rypl_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  132 bits (333), Expect = 7e-39
 Identities = 31/207 (14%), Positives = 76/207 (36%), Gaps = 9/207 (4%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + +    + G+++  + + T+     S + +++ +I+  +   +AG  +D          
Sbjct: 2   TTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGS 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
           Q + +    +E + V    + L +    Y          +  +  G+ +  G  +Y  D 
Sbjct: 62  QCRLHELREKERISVAAASKILSNLVYQYKGA----GLSMGTMICGYTRKEGPTIYYVDS 117

Query: 153 SGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLEL 212
            G         +G+    A  +L  +YK D+S E+A+ L  + +       + +   + L
Sbjct: 118 DGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNL 177

Query: 213 AEVFLMPSGKVKYQVCSPEALSKLLVK 239
             V      +  +       + +L  K
Sbjct: 178 YHV-----TEDGWIYHGNHDVGELFWK 199

>d1rypk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 198

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  127 bits (321), Expect = 3e-37
 Identities = 39/192 (20%), Positives = 71/192 (36%), Gaps = 9/192 (4%)

Query: 25  MEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDAN 84
           M+ I      +GI  +D V+L   K VT  +     S +K  ++  H   + AG   D  
Sbjct: 1   MDII------LGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTV 54

Query: 85  ILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNY- 143
                 +   Q Y+      +  + +   +   ++        RP+ V+ L  G+DK   
Sbjct: 55  QFAEYIQANIQLYSIREDYELSPQAVSSFVR--QELAKSIRSRRPYQVNVLIGGYDKKKN 112

Query: 144 GFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDST 203
             +LY  D  G        A G +     S+L   Y+ D++ EE + L    + +     
Sbjct: 113 KPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRM 172

Query: 204 SLTSDKLELAEV 215
            +    + +  V
Sbjct: 173 PMDFKGVIVKIV 184

>d1iruk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 199

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  125 bits (315), Expect = 2e-36
 Identities = 43/191 (22%), Positives = 68/191 (35%), Gaps = 8/191 (4%)

Query: 25  MEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDAN 84
           ME +      IGI   D V++  ++   S ++Q     +KM+K+ + +     G   D  
Sbjct: 1   MEYL------IGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTV 54

Query: 85  ILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYG 144
                 +   Q Y       +                 +     P+ V+ L AG+D++ G
Sbjct: 55  QFAEYIQKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSRT--PYHVNLLLAGYDEHEG 112

Query: 145 FQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTS 204
             LY  D          AA G       SIL + Y   ISRE AV+L  K L +      
Sbjct: 113 PALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEELQKRFI 172

Query: 205 LTSDKLELAEV 215
           L      +  +
Sbjct: 173 LNLPTFSVRII 183

>d1iru2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 217

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  124 bits (311), Expect = 1e-35
 Identities = 28/193 (14%), Positives = 65/193 (33%), Gaps = 6/193 (3%)

Query: 26  EAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANI 85
             +    S +G+  + GVV+  +   +   L    +  ++ ++++      +G  +D   
Sbjct: 3   NPMVTGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQY 62

Query: 86  LINTARVQAQRYTYAYQ-EPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYG 144
           L                        +   L      Y++   + P   + +  G+     
Sbjct: 63  LKQVLGQMVIDEELLGDGHSYSPRAIHSWLTR--AMYSRRSKMNPLWNTMVIGGYADGES 120

Query: 145 FQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKD--DISREEAVQLALKVLSKTMDS 202
           F L   D  G      + A G     AQ +L++  +    +S+ EA  L  + +      
Sbjct: 121 F-LGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYYR 179

Query: 203 TSLTSDKLELAEV 215
            + + ++ + A V
Sbjct: 180 DARSYNRFQTATV 192

>d1ryph_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 205

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  123 bits (309), Expect = 2e-35
 Identities = 33/209 (15%), Positives = 81/209 (38%), Gaps = 9/209 (4%)

Query: 28  IGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILI 87
           +    S + +  KDGV+L  + + T+     +  T+K+ ++ D + C  +G  +D   + 
Sbjct: 6   VSLGASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIA 65

Query: 88  NTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQL 147
           +  +   + YT  Y  P            +      +          + AG+D     ++
Sbjct: 66  DIVQYHLELYTSQYGTPSTET------AASVFKELCYENKDNLTAGIIVAGYDDKNKGEV 119

Query: 148 YMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTS 207
           Y     G+      A  G+ +        +++++++S+EE V      LS+ +     + 
Sbjct: 120 YTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQAIKWDGSSG 179

Query: 208 DKLELAEVFLMPSGKVKYQVCSPEALSKL 236
             + +    ++ +  V+  +  P+   +L
Sbjct: 180 GVIRMV---VLTAAGVERLIFYPDEYEQL 205

>d1iruj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 204

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  123 bits (308), Expect = 3e-35
 Identities = 19/188 (10%), Positives = 67/188 (35%), Gaps = 6/188 (3%)

Query: 30  NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINT 89
           N G+ + +  K+ V +  +++   +    +T  +K++ + D +   +AG+ +D   +   
Sbjct: 6   NGGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQR 65

Query: 90  ARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDK-NYGFQLY 148
            + +   Y       +    L+  + +            P+    + AG D   +   + 
Sbjct: 66  LKFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFG----PYYTEPVIAGLDPKTFKPFIC 121

Query: 149 MSDPSGNYGGWKAAAIGANN-QAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTS 207
             D  G         +     +    + +  ++ ++  +   +   + +   +D  +++ 
Sbjct: 122 SLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVDRDAVSG 181

Query: 208 DKLELAEV 215
             + +  +
Sbjct: 182 MGVIVHII 189

>d1q5qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Rhodococcus erythropolis [TaxId: 1833]} Length = 224

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

 Score =  119 bits (300), Expect = 6e-34
 Identities = 47/215 (21%), Positives = 85/215 (39%), Gaps = 8/215 (3%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + + +  K GV+L G+++ T   L  S   EK+Y  D++ A  +AG    A  L+    V
Sbjct: 2   TIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAV 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFG----GLRPFGVSFLFAGWDKNYGFQLY 148
           + + Y      P+  +     L    +G          + P  V +     D++   ++ 
Sbjct: 62  ELEHYEKIEGVPLTFDGKANRLASMVRGNLGAAMQGLAVVPLLVGYDLDADDESRAGRIV 121

Query: 149 MSDPSGNYGGWKA--AAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTM--DSTS 204
             D  G     +A   A+G+ +  A+S LK+ Y  D   E A++ A++ L      DS +
Sbjct: 122 SYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSDEETALRAAIESLYDAADDDSAT 181

Query: 205 LTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK 239
              D         +   +      S E  S+L  +
Sbjct: 182 GGPDLTRGIYPTAVTITQAGAVHVSEETTSELARR 216

>d1rypj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 204

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  118 bits (296), Expect = 1e-33
 Identities = 33/188 (17%), Positives = 67/188 (35%), Gaps = 7/188 (3%)

Query: 30  NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINT 89
           N G  + +  KD V +  + ++ S+ L  S   EK++    HV   + G+ +D   L   
Sbjct: 7   NGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHY-GHVFLGITGLATDVTTLNEM 65

Query: 90  ARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYG-FQLY 148
            R +   Y    +  +  E   Q +  +           P+ V  + AG +   G   + 
Sbjct: 66  FRYKTNLYKLKEERAIEPETFTQLVSSSLYERRF----GPYFVGPVVAGINSKSGKPFIA 121

Query: 149 MSDPSGNYGGWKA-AAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTS 207
             D  G     K     G  +     + +  Y+ ++  E+  +   + L    D  +L+ 
Sbjct: 122 GFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDALSG 181

Query: 208 DKLELAEV 215
               +  +
Sbjct: 182 WGAVVYII 189

>d1iru1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]} Length = 213

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  109 bits (274), Expect = 4e-30
 Identities = 36/195 (18%), Positives = 69/195 (35%), Gaps = 13/195 (6%)

Query: 30  NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINT 89
           N G+ + I  +D  ++  + +++      +  + K YK+ D      +G   D   L   
Sbjct: 8   NGGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKI 67

Query: 90  ARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYM 149
              + + Y ++  + M    +   L         F    P+ V  +  G D+     +Y 
Sbjct: 68  IEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFF----PYYVYNIIGGLDEEGKGAVYS 123

Query: 150 SDPSGNYGGWKAAAIGANNQAAQSILKQDYK---------DDISREEAVQLALKVLSKTM 200
            DP G+Y      A G+ +   Q +L                +S + A++L   V     
Sbjct: 124 FDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISAA 183

Query: 201 DSTSLTSDKLELAEV 215
           +    T D L +  V
Sbjct: 184 ERDVYTGDALRICIV 198

>d1m4ya_ d.153.1.4 (A:) HslV (ClpQ) protease {Thermotoga maritima [TaxId: 2336]} Length = 171

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: HslV (ClpQ) protease
species: Thermotoga maritima [TaxId: 2336]

 Score = 54.0 bits (129), Expect = 1e-09
 Identities = 27/164 (16%), Positives = 48/164 (29%), Gaps = 12/164 (7%)

Query: 33  SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARV 92
           + + +      V+ G+ +VT        +  K+ K+ +    A         + +     
Sbjct: 2   TILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFE 61

Query: 93  QAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDP 152
              R          VE       D      +           L    DK   F +   + 
Sbjct: 62  AKLREWGGNLTKAAVELAKDWRTDRVLRRLE----------ALLLVADKENIF-IISGNG 110

Query: 153 SGNYGGWKAAAIGANNQAAQSILK-QDYKDDISREEAVQLALKV 195
                   AAAIG+    A +  K      D+S  E V+ A+ +
Sbjct: 111 EVIQPDDDAAAIGSGGPYALAAAKALLRNTDLSAREIVEKAMTI 154

>d2z3ba1 d.153.1.4 (A:1-180) HslV (ClpQ) protease {Bacillus subtilis [TaxId: 1423]} Length = 180

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: HslV (ClpQ) protease
species: Bacillus subtilis [TaxId: 1423]

 Score = 54.0 bits (129), Expect = 1e-09
 Identities = 21/186 (11%), Positives = 49/186 (26%), Gaps = 10/186 (5%)

Query: 30  NAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINT 89
           +A +   +  K    + G+ +VT         T +  +   +            ++    
Sbjct: 4   HATTIFAVQHKGRSAMSGDGQVTFGQAVVMKHTARKVRKLFNGKVLAGF---AGSVADAF 60

Query: 90  ARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYM 149
              +                 V+   + +             V         +   ++  
Sbjct: 61  TLFEKFEAKLEEYNGNLKRAAVELAKEWRSDKVLRKLEAMLIVMNQDTLLLVSGTGEVIE 120

Query: 150 SDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDK 209
             P          AIG+    A +  +   K       A ++A   L    +    T+D+
Sbjct: 121 --PDDGI-----LAIGSGGNYALAAGRALKKHAGESMSASEIARAALETAGEICVYTNDQ 173

Query: 210 LELAEV 215
           + L E+
Sbjct: 174 IILEEL 179

>d1g3ka_ d.153.1.4 (A:) HslV (ClpQ) protease {Haemophilus influenzae [TaxId: 727]} Length = 173

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: HslV (ClpQ) protease
species: Haemophilus influenzae [TaxId: 727]

 Score = 49.8 bits (118), Expect = 4e-08
 Identities = 21/163 (12%), Positives = 49/163 (30%), Gaps = 14/163 (8%)

Query: 35  IGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDH-VACAVAGIMSDANILINTARVQ 93
           + +     VV+ G+ +V+        +  K+ ++ +  V    AG  +DA  L      +
Sbjct: 4   VSVRRNGQVVVGGDGQVSLGNTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFE--LFE 61

Query: 94  AQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPS 153
            +   +         +L +     +             +  +    D+     +      
Sbjct: 62  RKLEMHQGHLLKSAVELAKDWRTDRALR---------KLEAMLIVADEKESLIITGIGDV 112

Query: 154 GNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVL 196
                 +  AIG+    A S        + +   A ++  K L
Sbjct: 113 VQPEEDQILAIGSGGNYALSA--ARALVENTELSAHEIVEKSL 153

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	250
d1iruc_	250	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypc_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rypb_	250	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irug_	245	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1irua_	244	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1j2pa_	243	Proteasome alpha subunit (non-catalytic) {Archaeon	100.0
d1rypd_	241	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1irue_	234	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1irud_	243	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1iruf_	238	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1irub_	233	Proteasome alpha subunit (non-catalytic) {Cow (Bos	100.0
d1rypa_	243	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rypf_	233	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rypg_	244	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1rype_	242	Proteasome alpha subunit (non-catalytic) {Baker's	100.0
d1yara1	221	Proteasome alpha subunit (non-catalytic) {Archaeon	100.0
d1q5qa_	227	Proteasome alpha subunit (non-catalytic) {Rhodococ	100.0
d1yarh1	203	Proteasome beta subunit (catalytic) {Archaeon Ther	100.0
d1ryph_	205	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1irul_	201	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1j2qh_	202	Proteasome beta subunit (catalytic) {Archaeon Arch	100.0
d1rypk_	198	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1rypl_	212	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1iruh_	202	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1irui_	220	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1ryp2_	233	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1iruj_	204	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1ryp1_	222	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1rypj_	204	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1rypi_	222	Proteasome beta subunit (catalytic) {Baker's yeast	100.0
d1q5qh_	224	Proteasome beta subunit (catalytic) {Rhodococcus e	100.0
d1iru2_	217	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1iru1_	213	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d1iruk_	199	Proteasome beta subunit (catalytic) {Cow (Bos taur	100.0
d2z3ba1	180	HslV (ClpQ) protease {Bacillus subtilis [TaxId: 14	99.93
d1m4ya_	171	HslV (ClpQ) protease {Thermotoga maritima [TaxId:	99.91
d1g3ka_	173	HslV (ClpQ) protease {Haemophilus influenzae [TaxI	99.91

>d1iruc_ d.153.1.4 (C:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=4.4e-65  Score=432.11  Aligned_cols=245  Identities=59%  Similarity=0.977  Sum_probs=233.5

Q ss_pred             CCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchH
Q 025640            2 SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMS   81 (250)
Q Consensus         2 ~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~   81 (250)
                      |++||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.++++++.+++.+||++|+++++|+++|..+
T Consensus         1 ~~~yd~~~t~fsp~Grl~QvEyA~kav~~G~tvvgik~~dgVvlaad~~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~   80 (250)
T d1iruc_           1 SRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFFSEKIYKLNEDMACSVAGITS   80 (250)
T ss_dssp             CTTTCCCTTCCCTTSCCHHHHHHHHHHTTSCCEEEEBCSSEEEEEECCCCCCTTBCCCSSCSSEEECSSSEEEEEEECHH
T ss_pred             CCccCCCCeeECCCCcchHHHHHHHHHhcCCcEEEEEeCCEEEEEEeCccccCCcccCcccceEEECCCcEEEEeecccc
Confidence            78999999999999999999999999999999999999999999999999999999888889999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceE
Q 025640           82 DANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKA  161 (250)
Q Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~  161 (250)
                      |++.+.+.++.++..|++.++.+++++.+++.++..++.+++++++|||++++||+|||+++||+||.+||+|++.++++
T Consensus        81 D~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~~~~~~~rP~~~~~li~G~D~~~gp~Ly~~Dp~G~~~~~~~  160 (250)
T d1iruc_          81 DANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKA  160 (250)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBSSCCCCCEEEEEEEEETTTEEEEEEEETTTEEEECSE
T ss_pred             hHHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhhccCCcceEEEEEEEEcCCCCCEEEEEcccccEeeeeE
Confidence            99999999999999999999999999999999999999999999999999999999999877899999999999999999


Q ss_pred             EEEeCChHHHHHHHHhhCCC-CCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 025640          162 AAIGANNQAAQSILKQDYKD-DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH  240 (250)
Q Consensus       162 ~a~G~g~~~~~~~L~~~~~~-~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~  240 (250)
                      +|+|.|+++++++|++.|++ +|+++||++++++||+.+.+++..++++++|++|++++ ++..++.++++||+.++.++
T Consensus       161 ~a~G~gs~~a~~~Le~~y~~~~ms~eeai~la~~al~~~~~~d~~~~~~iei~ii~~~~-~~~~~~~l~~~Ei~~~l~~~  239 (250)
T d1iruc_         161 TCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTREN-GKTVIRVLKQKEVEQLIKKH  239 (250)
T ss_dssp             EEESTTTTHHHHHHHHHCCTTCCCHHHHHHHHHHHHHHSSSCTTCCSTTCEEEEEECCS-SSCEEEECCHHHHHHHHHHH
T ss_pred             EEeCcChHHHHHHHHhhcccCCCCHHHHHHHHHHHHHHHhcccCCCCCeEEEEEEEcCC-CceeEEECCHHHHHHHHHHH
Confidence            99999999999999999985 89999999999999999999999999999999999987 33458999999999999887


Q ss_pred             CCCCccc
Q 025640          241 GVTQPAA  247 (250)
Q Consensus       241 ~~~~~~~  247 (250)
                      .+...++
T Consensus       240 ~e~~~~a  246 (250)
T d1iruc_         240 EEEEAKA  246 (250)
T ss_dssp             HTTTTTT
T ss_pred             HHHhhhH
Confidence            7554443

>d1rypc_ d.153.1.4 (C:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.8e-63  Score=419.59  Aligned_cols=240  Identities=61%  Similarity=0.998  Sum_probs=230.9

Q ss_pred             CCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchH
Q 025640            2 SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMS   81 (250)
Q Consensus         2 ~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~   81 (250)
                      |++||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.++++++.+++.+||++|+++++++++|.++
T Consensus         2 ~~~yd~~~t~fsp~G~~~Qveya~~ai~~G~T~vgi~~~dgVvlaad~r~s~~~~~~~~~~~KI~~i~~~i~~~~sG~~~   81 (244)
T d1rypc_           2 SRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTA   81 (244)
T ss_dssp             CGGGCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECSSCCSSBCSTTCCSSEEESSSSEEEEEEECHH
T ss_pred             CCccCCCceeECCCCcChHHHHHHHHHhcCCCEEEEEeCCEEEEEEeCCccCCCcccCCccceEEEcCCCeEEEEecccC
Confidence            68999999999999999999999999999999999999999999999999999999888899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceE
Q 025640           82 DANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKA  161 (250)
Q Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~  161 (250)
                      |++.+.+.++.++..+++.++.+++++.+++.++..++.++++.++|||++++||+|||+++||+||.+||.|++.++++
T Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~rP~~~~~ll~G~d~~~gp~Ly~id~~Gs~~~~~~  161 (244)
T d1rypc_          82 DAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKA  161 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSCCCCCEEEEEEEEETTTEEEEEEECTTCCEEEBSE
T ss_pred             cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhhhhccccCccceeEEEEEEecCCCceEEEecCCCcEeeeee
Confidence            99999999999999999999999999999999999999999999999999999999999877899999999999999999


Q ss_pred             EEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCC-CceeEEECCHHHHHHHHHHh
Q 025640          162 AAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPS-GKVKYQVCSPEALSKLLVKH  240 (250)
Q Consensus       162 ~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~-~~~~~~~~~~~ei~~~~~~~  240 (250)
                      +|+|+|+.+++++|++.|+++|+++||++++++||+.+.+++..++++++|++|++++. +...++.++++||+.++.+.
T Consensus       162 ~a~G~g~~~a~~~Le~~~~~~ms~eeai~l~~~al~~a~~~d~~~~~~iei~ii~~~~~~~~~~~~~~~~~Ei~~~l~k~  241 (244)
T d1rypc_         162 ISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKT  241 (244)
T ss_dssp             EEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSSSSCCGGGEEEEEEECCSSSSSCEEEECCHHHHHHHHHHH
T ss_pred             eeccchhHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEECCCcccceeEEECCHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999998873 23357899999999999887


Q ss_pred             C
Q 025640          241 G  241 (250)
Q Consensus       241 ~  241 (250)
                      +
T Consensus       242 ~  242 (244)
T d1rypc_         242 G  242 (244)
T ss_dssp             T
T ss_pred             C
Confidence            5

>d1rypb_ d.153.1.4 (B:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1e-62  Score=417.56  Aligned_cols=238  Identities=33%  Similarity=0.556  Sum_probs=223.6

Q ss_pred             CCCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         1 ~~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      |+.+||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|+|.+++++.. ++.+||++|+++++|+++|..
T Consensus         1 m~~~yd~~~t~fsp~G~l~QvEyA~kav~~G~tvvgi~~~dgVvlaad~r~~~~~~~~-~~~~ki~~I~~~i~~~~sG~~   79 (250)
T d1rypb_           1 MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMS-ETLSKVSLLTPDIGAVYSGMG   79 (250)
T ss_dssp             CCCCCCSBSSCBCTTSCBHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSCSSBCG-GGCCSSEEEETTEEEEEEECH
T ss_pred             CCccccCCCceECCCCeehHHHHHHHHHHcCCCEEEEEeCCEEEEEEecccCCccccc-cccceeEeccCCEEEEeeecc
Confidence            9999999999999999999999999999999999999999999999999999887764 578999999999999999999


Q ss_pred             HHHHHHHHHHHHHHH-HHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecc
Q 025640           81 SDANILINTARVQAQ-RYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW  159 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~-~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~  159 (250)
                      +|++.+.+.++.++. +|...++.+++++.+++.++++++.++++.+.|||++++||+|||+..||+||++||.|++.++
T Consensus        80 ~D~~~l~~~~~~~~~~~y~~~~~~~~~~~~la~~~~~~~~~~~~~~~~rp~~v~~li~G~D~~~gp~Ly~id~~G~~~~~  159 (250)
T d1rypb_          80 PDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPW  159 (250)
T ss_dssp             HHHHHHHHHHHHHHHHTTHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCCEEEEEEEEETTTEEEEEEECTTSCEEEB
T ss_pred             cHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhhhcCCcCeeEEEEEEEecCCCCCEEEEEcCcEEEEEe
Confidence            999999999999886 4889999999999999999999999999999999999999999998779999999999999999


Q ss_pred             eEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCC-----------CceeEEEC
Q 025640          160 KAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPS-----------GKVKYQVC  228 (250)
Q Consensus       160 ~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~-----------~~~~~~~~  228 (250)
                      +++|+|+|+.+++++|++.|+++|+++||++++++||+.+.+++ .++.+++|++|++++.           ....|+++
T Consensus       160 ~~~a~G~gs~~a~~~Le~~~~~~ms~eea~~la~~al~~~~~~d-~s~~~iev~vi~~~~~~~~~~~~v~~~~~~~fr~l  238 (250)
T d1rypb_         160 KATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEGE-FNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKL  238 (250)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCCSC-CSTTTEEEEEECSCCGGGTSEESCSSCCCCSEEEC
T ss_pred             eEEecCcchHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHhhcc-CCCCCEEEEEEeCCCcccccccccccccCCceEEC
Confidence            99999999999999999999999999999999999999999876 5789999999998752           12358999


Q ss_pred             CHHHHHHHHHHh
Q 025640          229 SPEALSKLLVKH  240 (250)
Q Consensus       229 ~~~ei~~~~~~~  240 (250)
                      +++||+++++.+
T Consensus       239 s~eei~~~l~~l  250 (250)
T d1rypb_         239 TSQEINDRLEAL  250 (250)
T ss_dssp             CHHHHHHHHTTC
T ss_pred             CHHHHHHHHHhC
Confidence            999999998753

>d1irug_ d.153.1.4 (G:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=8.5e-63  Score=416.52  Aligned_cols=239  Identities=34%  Similarity=0.529  Sum_probs=222.9

Q ss_pred             CCCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            1 MSRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         1 ~~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      |-++||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.+++++.. ++.+||++|+++++|++||..
T Consensus         3 ~~~~yd~~~t~Fsp~Grl~QvEYa~~av~~G~t~VGik~~dgVvlaad~~~~~~~~~~-~~~~Ki~~I~~~i~~~~sG~~   81 (245)
T d1irug_           3 IGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEE-GSNKRLFNVDRHVGMAVAGLL   81 (245)
T ss_dssp             CCSSTTSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSBEEEEEEEECSCTTBCT-TTTCCEEEEETTEEEEEEECH
T ss_pred             CccccCCCCceECCCCeehHHHHHHHHHHcCCcEEEEEeCCEEEEEEecccccccccc-CccceEEEcCCCEEEEeccCc
Confidence            5679999999999999999999999999999999999999999999999998888764 477999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce
Q 025640           81 SDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK  160 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~  160 (250)
                      +|++.+.+.++.++..|++.++.+++++.+++.|++.+|.|+++++.|||+|++||+|||+++||+||.+||+|++.+++
T Consensus        82 ~D~~~l~~~~~~~~~~~~~~~g~~i~~~~la~~la~~~~~~t~~~~~rP~~vs~li~G~D~~~gp~Ly~iDp~G~~~~~~  161 (245)
T d1irug_          82 ADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYW  161 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSBSSBCCCSEEEEEEEEETTTEEEEEEECTTCCEEEBS
T ss_pred             hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhccccccccceEEEEEEEcCCCCceEEEEcCCceEEeee
Confidence            99999999999999999999999999999999999999999999999999999999999987799999999999999999


Q ss_pred             EEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 025640          161 AAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH  240 (250)
Q Consensus       161 ~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~  240 (250)
                      ++|+|.|++.++++|++.|+++||.+||++++++||+.+.+++...+.+++|++|+++.++   ++.+.++|+...+.++
T Consensus       162 ~~a~G~gs~~a~~~Le~~~~~dmt~eea~~l~~~~l~~~~~~~~~~~~~iei~~v~~~~~~---~~~~~~~e~~~~~~~~  238 (245)
T d1irug_         162 GCAIGKARQAAKTEIEKLQMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNG---RHEIVPKDIREEAEKY  238 (245)
T ss_dssp             EEEESTTHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHSCSSSSCCEEEEEEECBTTTTT---CCEECCHHHHHHHHHH
T ss_pred             EEEECCccHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEEEEecCCC---eEEEChHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999888888889999999987533   4566677777776665


Q ss_pred             CCC
Q 025640          241 GVT  243 (250)
Q Consensus       241 ~~~  243 (250)
                      .+.
T Consensus       239 ~~~  241 (245)
T d1irug_         239 AKE  241 (245)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>d1irua_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=1.3e-61  Score=409.23  Aligned_cols=236  Identities=34%  Similarity=0.597  Sum_probs=221.9

Q ss_pred             CCCCCCCccccCCCCcccccchHHHHhcCCc-cEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCch
Q 025640            2 SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAG-SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIM   80 (250)
Q Consensus         2 ~~~yd~~~~~f~p~G~l~qveya~~a~~~g~-t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~   80 (250)
                      +.+||+++|+|||||||+|||||+||+++|+ |+|||+++||||||+|+|.++++.+.+ +.+||++|++|++|+++|..
T Consensus         5 ~~gyd~~~t~Fsp~Grl~QvEYA~kav~~gg~t~igIk~~dgVVlaad~r~~~~~~~~~-~~~KI~~I~~~i~~~~sG~~   83 (244)
T d1irua_           5 SAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSS-TVTHLFKITENIGCVMTGMT   83 (244)
T ss_dssp             CCTTTTTSSCCCTTSCCHHHHHHHHHHHTTCCEEEEEECSSEEEEEEECCCCCSSBCGG-GCCSEEESSSSCEEEEEECH
T ss_pred             CCCcCCCCceECCCCeEhHHHHHHHHHHhCCccEEEEEcCCEEEEEEecccccccccCC-ccceEEEecCCcEEEEecch
Confidence            4589999999999999999999999999976 899999999999999999987777754 78999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecce
Q 025640           81 SDANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWK  160 (250)
Q Consensus        81 ~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~  160 (250)
                      +|++.+.+.++.++..|++.++.+++++.+++.++.+++.++++++.|||+|++||+|||+++||+||.+||+|++.+++
T Consensus        84 ~D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~rP~~v~~ll~G~D~~~g~~Ly~~Dp~G~~~~~~  163 (244)
T d1irua_          84 ADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFK  163 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBSSBCCCSEEEEEEEEETTTEEEEEEECTTSCEEEBS
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHhcccccCccceeeEEEEEcCCCCcEEEEEcCCccEEecc
Confidence            99999999999999999999999999999999999999999999999999999999999987789999999999999999


Q ss_pred             EEEEeCChHHHHHHHHhhCC--CCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 025640          161 AAAIGANNQAAQSILKQDYK--DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLV  238 (250)
Q Consensus       161 ~~a~G~g~~~~~~~L~~~~~--~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~  238 (250)
                      ++|+|.|+..++++||++|+  ++|+++||++++++||+.+.+++. .+++++|++|++++   ..+++++++||+.++.
T Consensus       164 ~~a~G~gs~~~~~~Le~~~~~~~d~t~eeai~l~~~~l~~~~~~d~-~~~~iev~ii~~~~---~~~~~l~~~ei~~~l~  239 (244)
T d1irua_         164 ATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDF-KPSEIEVGVVTVEN---PKFRILTEAEIDAHLV  239 (244)
T ss_dssp             EEEEETTHHHHHHHHHHHTTSCCCCCHHHHHHHHHHHHHHHTTCCC-CTTSEEEEEEETTE---EEEEECCHHHHHHHHH
T ss_pred             eEeccCchhHHHHHHHhccccccCCCHHHHHHHHHHHHHHHHhcCC-CCCcEEEEEEEeCC---CcEEECCHHHHHHHHH
Confidence            99999999999999999994  589999999999999999999774 56789999999886   3589999999999998


Q ss_pred             HhCC
Q 025640          239 KHGV  242 (250)
Q Consensus       239 ~~~~  242 (250)
                      .+.+
T Consensus       240 ~~~~  243 (244)
T d1irua_         240 ALAE  243 (244)
T ss_dssp             HHHT
T ss_pred             HHhc
Confidence            8765

>d1j2pa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=100.00  E-value=3.4e-61  Score=406.43  Aligned_cols=235  Identities=40%  Similarity=0.712  Sum_probs=222.4

Q ss_pred             CCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHH
Q 025640            4 RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDA   83 (250)
Q Consensus         4 ~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~   83 (250)
                      +||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|+|.+++++.. .+.+||++|+++++|++||..+|+
T Consensus         4 gyd~~~t~fsp~Grl~QvEya~kav~~G~t~Igik~~dgVvlaad~r~~~~~~~~-~~~~KI~~I~~~i~~~~sG~~~D~   82 (243)
T d1j2pa_           4 GYDRAITVFSPDGRLFQVEYAREAVKRGATAIGIKCKEGVILIADKRVGSKLLEK-DTIEKIYKIDEHICAATSGLVADA   82 (243)
T ss_dssp             TSSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEECCCSCTTBCG-GGCCSEEECSSSEEEEEEECHHHH
T ss_pred             CcCCCCccCCCCCcchHHHHHHHHHHcCCCEEEEEECCEEEEEEecCccccCccc-cccccEeecCCcEEEEeeecccHH
Confidence            7999999999999999999999999999999999999999999999999998765 477999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEE
Q 025640           84 NILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAA  163 (250)
Q Consensus        84 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a  163 (250)
                      +.+.+.++.++..|++.++.+++++.+++.++..+|.++++.+.|||++++|+||+|+  +|+||.+||+|++.+++++|
T Consensus        83 ~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~rP~~~~~il~G~D~--~p~Ly~~Dp~G~~~~~~~~a  160 (243)
T d1j2pa_          83 RVLIDRARIEAQINRLTYDIPITVKELAKKICDFKQQYTQYGGVRPFGVSLLIAGVNE--VPKLYETDPSGALLEYKATA  160 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEESS--SEEEEEECTTCCEEEBSEEE
T ss_pred             HHHHHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHHHHhhhccCCccceeEEEEEecC--CceEEEEeccCceeeeeEEE
Confidence            9999999999999999999999999999999999999999999999999999999986  59999999999999999999


Q ss_pred             EeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhCCC
Q 025640          164 IGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVT  243 (250)
Q Consensus       164 ~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~~  243 (250)
                      +|.|+.+++++|++.|+++||++||++++++||+.+.+++. +++++||+++++++.   .|++++++||+.++.++.+.
T Consensus       161 ~G~g~~~a~~~Le~~y~~~ms~eeai~la~~~l~~~~~~d~-~~~~iei~iv~~~~~---~~~~l~~~ei~~~~~~~~e~  236 (243)
T d1j2pa_         161 IGMGRMAVTEFFEKEYRDDLSFDDAMVLGLVAMGLSIESEL-VPENIEVGYVKVDDR---TFKEVSPEELKPYVERANER  236 (243)
T ss_dssp             ESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHTSCC-CGGGEEEEEEETTTC---CCEECCHHHHHHHHHHHHHH
T ss_pred             eCCCcHHHHHHHHhhcccCCCHHHHHHHHHHHHHHHHhccc-CCCceEEEEEEeCCC---cEEECCHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999764 567899999998763   38999999999999887654


Q ss_pred             Cc
Q 025640          244 QP  245 (250)
Q Consensus       244 ~~  245 (250)
                      .+
T Consensus       237 ~~  238 (243)
T d1j2pa_         237 IR  238 (243)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>d1rypd_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=5.6e-61  Score=404.74  Aligned_cols=236  Identities=35%  Similarity=0.589  Sum_probs=223.4

Q ss_pred             CCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHH
Q 025640            4 RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDA   83 (250)
Q Consensus         4 ~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~   83 (250)
                      +||+++|+|||||||+|||||.||+++|+|+|||+++||||||+|++.++++++.+.+.+||++|++|++|++||..+|+
T Consensus         1 gyd~~~t~fsp~Grl~QvEya~kav~~G~tvIgik~~dgVvlaad~~~~~~~~~~~~~~~KI~~I~~~i~~~~sG~~~D~   80 (241)
T d1rypd_           1 GYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFSGLNADS   80 (241)
T ss_dssp             CCCCCCSCCBTTTBCHHHHHHHHHHTTSCCEEEEECSSCEEEEEECCCSSCCBCTTTSCCSEEEEETTEEEEEEECHHHH
T ss_pred             CCCCCCceECCCCcEeHHHHHHHHHHcCCCEEEEEeCCEEEEEEEccccccCcccccccccEEEeCCCEEEEeeeccchH
Confidence            69999999999999999999999999999999999999999999999999999888888999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCC-CCeEEEEECCCCceecceEE
Q 025640           84 NILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKN-YGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        84 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~-~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      +.+.+.++.++..|++.++.+++++.+++.++.+++.++++.+.|||+|++||||||+. ++|+||.+||+|++.+++++
T Consensus        81 ~~l~~~~~~~~~~~~~~~~~~i~~~~la~~i~~~~~~~t~~~~~rP~~v~~li~G~d~~~~~p~Ly~idp~G~~~~~~~~  160 (241)
T d1rypd_          81 RILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQ  160 (241)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSSTTBCCCSEEEEEEECCTTCCSCEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHhhccccCcccceEEEEEEccccCcceEEEecCCEEEEeeCeE
Confidence            99999999999999999999999999999999999999999999999999999999964 58999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhCC---CCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          163 AIGANNQAAQSILKQDYK---DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~~---~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      |+|.|++.++++|++.|+   ++|+++|+++++++||+.+.++   ++.+++|+++++++    .+++++++||+.++.+
T Consensus       161 a~G~gs~~~~~~Le~~~~~~~~~~t~~e~i~lal~al~~~~~~---~~~~iei~ii~~d~----~~~~l~~~ei~~~l~~  233 (241)
T d1rypd_         161 TIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQT---GAKNIEITVVKPDS----DIVALSSEEINQYVTQ  233 (241)
T ss_dssp             EESTTHHHHHHHHHTTCCTTSCCCSHHHHHHHHHHHHHHHHCS---CSTTEEEEEEETTT----EEEECCHHHHHHHHHH
T ss_pred             EECcCHHHHHHHHHHhhhcccCCCCHHHHHHHHHHHHHHHhcC---CCCcEEEEEEECCC----CEEECCHHHHHHHHHH
Confidence            999999999999999996   4699999999999999998864   46789999999886    4899999999999999


Q ss_pred             hCCCCcc
Q 025640          240 HGVTQPA  246 (250)
Q Consensus       240 ~~~~~~~  246 (250)
                      +.+.+.+
T Consensus       234 i~~~~~~  240 (241)
T d1rypd_         234 IEQEKQE  240 (241)
T ss_dssp             HTHHHHC
T ss_pred             HHHHHhc
Confidence            8654433

>d1irue_ d.153.1.4 (E:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=8e-61  Score=402.16  Aligned_cols=229  Identities=38%  Similarity=0.652  Sum_probs=216.9

Q ss_pred             CCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHH
Q 025640            5 YDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDAN   84 (250)
Q Consensus         5 yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~   84 (250)
                      ||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.+.+++.. ++.+||++|+++++|+++|..+|++
T Consensus         1 yd~~~t~fsp~G~l~QvEYa~kav~~G~t~vgik~~dgVvlaad~~~~~~~~~~-~~~~KI~~I~~~i~~~~sG~~~D~~   79 (234)
T d1irue_           1 YDRGVNTFSPEGRLFQVEYDIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEP-SSIEKIVEIDAHIGCAMSGLIADAK   79 (234)
T ss_dssp             CCCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEEETTEEEEEEECCCCCTTBCT-TSCCSEEEEETTEEEEEEECHHHHH
T ss_pred             CCCCCceECCCCcchHHHHHHHHHHcCCCEEEEEeCCEEEEEEecCccCCCccc-CcccCEEEccCcEEEEEeeccchHH
Confidence            999999999999999999999999999999999999999999999999887764 5778999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCC-----CcceeEEEEEEEEeCCCCeEEEEECCCCceecc
Q 025640           85 ILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGG-----LRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW  159 (250)
Q Consensus        85 ~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~-----~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~  159 (250)
                      .+.+.++.++..|++.++.+++++.+++.|++++|.|+++.+     .|||+|++|+||||++ ||+||.+||.|++.++
T Consensus        80 ~l~~~~~~~~~~~~~~~~~~i~~~~la~~i~~~~~~~t~~~~~~~~~~rP~~~~~il~G~D~~-gp~Ly~idp~G~~~~~  158 (234)
T d1irue_          80 TLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDEK-GPQLFHMDPSGTFVQC  158 (234)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCBCSTTCCSSCBSSCCCEEEEEEEEETT-EEEEEEECTTSCEEEB
T ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhhcccccccccccceEEEEEEEEcCC-CCEEEEEecCccccee
Confidence            999999999999999999999999999999999999998865     7999999999999985 8999999999999999


Q ss_pred             eEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          160 KAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       160 ~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      +++|+|+|+++++++||+.|+++|+++||++++++||+.+.+++ .++.+++|++|++++    .|++++++||+.++.+
T Consensus       159 ~~~a~G~gs~~~~~~Le~~~~~~~~~eeai~~a~~al~~~~~~~-~~~~~iei~ii~~~~----~~k~l~~~ei~~~l~~  233 (234)
T d1irue_         159 DARAIGSASEGAQSSLQELYHKSMTLKEAIKSSLIILKQVMEEK-LNATNIELATVQPGQ----NFHMFTKEELEEVIKD  233 (234)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSSC-CCTTSEEEEEECSSS----CCEECCHHHHHHHHTT
T ss_pred             eeEEeCCchHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHhcc-CCCCCEEEEEEECCC----CEEECCHHHHHHHHHh
Confidence            99999999999999999999999999999999999999998754 677889999998775    4899999999999875


Q ss_pred             h
Q 025640          240 H  240 (250)
Q Consensus       240 ~  240 (250)
                      +
T Consensus       234 i  234 (234)
T d1irue_         234 I  234 (234)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1irud_ d.153.1.4 (D:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=4.2e-61  Score=405.93  Aligned_cols=238  Identities=36%  Similarity=0.600  Sum_probs=221.1

Q ss_pred             CCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHH
Q 025640            4 RYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDA   83 (250)
Q Consensus         4 ~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~   83 (250)
                      +||+++|+|||||||+|||||.||+++|+|+|||+++||||||+|++.+..+ ..+++.+||++|+++++|++||..+|+
T Consensus         1 ~yd~~~t~Fsp~Grl~QvEya~kav~~G~Tvvgik~~dgVvla~d~r~~~~~-~~~~~~~KI~~i~~~i~~~~sG~~~D~   79 (243)
T d1irud_           1 SYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKL-QDERTVRKICALDDNVCMAFAGLTADA   79 (243)
T ss_dssp             CCCCCCSCCCTTSCCHHHHHHHHHHHTSCCEEEECCSSEEEEEECCCCCCSS-SCGGGGCSEEESSSSCEEEEEECHHHH
T ss_pred             CCCCCCeeECCCCcchHHHHHHHHHhcCCCEEEEEeCCEEEEEEeccccCcc-cCCCccccEEECCCCEEEEEEEchhhH
Confidence            5999999999999999999999999999999999999999999999976444 445688999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEE
Q 025640           84 NILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAA  163 (250)
Q Consensus        84 ~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a  163 (250)
                      +.+.+.++.++..|++.++.+++++.+++.+++++|.++++++.||+++++||+|||++++|+||.+||+|++.+++++|
T Consensus        80 ~~l~~~~~~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~rp~~v~~li~G~D~~~~p~Ly~idp~G~~~~~~~~a  159 (243)
T d1irud_          80 RIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANA  159 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHTTSBTTBCCCCEEEEEEEECSSSCEEEEEECTTSCEEEBSEEE
T ss_pred             HHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHhcccCCccceEEEEEEEcCCCCCEEEEecCcEEEEeccEEE
Confidence            99999999999999999999999999999999999999999999999999999999987789999999999999999999


Q ss_pred             EeCChHHHHHHHHhhCCCCC--CHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhC
Q 025640          164 IGANNQAAQSILKQDYKDDI--SREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHG  241 (250)
Q Consensus       164 ~G~g~~~~~~~L~~~~~~~~--s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~  241 (250)
                      +|+|+..++++|++.|+++|  +.++++++++++|.....   .++.+++|++|++++    .|++++++||+.++..+.
T Consensus       160 ~G~gs~~a~~~Lek~~~~~~~~~~~~~i~~ai~~l~~~~~---~~~~~vei~ii~k~~----~~~~l~~~eI~~~l~~i~  232 (243)
T d1irud_         160 IGRGAKSVREFLEKNYTDEAIETDDLTIKLVIKALLEVVQ---SGGKNIELAVMRRDQ----SLKILNPEEIEKYVAEIE  232 (243)
T ss_dssp             ESTTHHHHHHHHTTTCCSSTTCSHHHHHHHHHHHHHTTSC---TTSTTCCEEEEESSS----CEECCCHHHHHHHTTTTT
T ss_pred             ECCChHHHHHHHHHhcccCCCccHHHHHHHHHHHHHHHhc---CCCCcEEEEEEECCC----CEEECCHHHHHHHHHHHH
Confidence            99999999999999999988  677788888888776654   457799999999875    489999999999999999


Q ss_pred             CCCccccC
Q 025640          242 VTQPAAET  249 (250)
Q Consensus       242 ~~~~~~~~  249 (250)
                      +.+++|++
T Consensus       233 ~~~~~~~~  240 (243)
T d1irud_         233 KEKEENEK  240 (243)
T ss_dssp             TTTTTTTS
T ss_pred             hhhhhhhh
Confidence            88877765

>d1iruf_ d.153.1.4 (F:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=3.8e-61  Score=405.00  Aligned_cols=233  Identities=31%  Similarity=0.526  Sum_probs=220.3

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      .+||+++|+|||||||+|||||.||+++|+|+|||+++||||||+|++.++++..   +.+||++|+++++|++||..+|
T Consensus         1 ~~yd~~~tiFsp~Grl~QvEYA~kav~~G~t~vgik~~dgVvlaad~~~~~~~~~---~~~KI~~I~~~i~~~~sG~~~D   77 (238)
T d1iruf_           1 NQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAA---HQKKILHVDNHIGISIAGLTAD   77 (238)
T ss_dssp             CTTTSCTTCCCTTSCCHHHHHHHHHHHHSCCEEEEECSSEEEEEEECCCSSTTBC---CCCCEEEEETTEEEEEEECHHH
T ss_pred             CCCCCCCeeECCCCcchHHHHHHHHHhcCCCEEEEEeCCEEEEEEecccccCCCC---ccceEEEeCCceEEEEeccchH
Confidence            4799999999999999999999999999999999999999999999999999864   4579999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+.++.++..|++.++.+++++.+++.|+...|.|+++.+.|||++++||||||+ .||+||++||+|++.+++++
T Consensus        78 ~~~l~~~~~~~~~~~~~~~~~~i~~~~l~~~l~~~~~~y~~~~~~rP~~v~~il~G~D~-~gp~Ly~~D~~G~~~~~~~~  156 (238)
T d1iruf_          78 ARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDD-MGPHIFQTCPSANYFDCRAM  156 (238)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEET-TEEEEEEECSSSCEEEESEE
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhhccCCCcccceEEEEEEcC-CCceEEEEcCCCCEEeeeeE
Confidence            99999999999999999999999999999999999999999999999999999999998 58999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhCCCCC--CHHHHHHHHHHHHHHhhcCC-CCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          163 AIGANNQAAQSILKQDYKDDI--SREEAVQLALKVLSKTMDST-SLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~~~~~--s~~ea~~l~~~~l~~~~~~~-~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      |+|.|+..++++|+++|+++|  +++||++++++||+.+..++ ..++.+|+|++|++++    .|++++++||+.++..
T Consensus       157 a~G~g~~~~~~~Lek~~~~~~~~~~~eav~lai~al~~~~~~~~~~~~~~iev~ii~k~~----~~~~l~~~ei~~~l~~  232 (238)
T d1iruf_         157 SIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDL----EFTIYDDDDVSPFLEG  232 (238)
T ss_dssp             EESTTHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCTTCCCCTTTEEEEEEETTE----EEEEECSGGGHHHHTT
T ss_pred             EECCCchhhHHHHHhhcccccCCCHHHHHHHHHHHHHHHHhhcccCCCCcEEEEEEeCCC----CEEECCHHHHHHHHHH
Confidence            999999999999999999854  99999999999999987655 4688999999999885    5899999999999988


Q ss_pred             hCCC
Q 025640          240 HGVT  243 (250)
Q Consensus       240 ~~~~  243 (250)
                      +.+.
T Consensus       233 i~ek  236 (238)
T d1iruf_         233 LEER  236 (238)
T ss_dssp             CCCC
T ss_pred             HHhC
Confidence            8763

>d1irub_ d.153.1.4 (B:) Proteasome alpha subunit (non-catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=3.6e-60  Score=397.82  Aligned_cols=231  Identities=37%  Similarity=0.627  Sum_probs=221.3

Q ss_pred             CCCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchH
Q 025640            2 SRRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMS   81 (250)
Q Consensus         2 ~~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~   81 (250)
                      +|+||+++|+|||||||+|||||.||+++|+|+|||+++||||||+|++.+++++. .++.+|||+|+++++|+++|..+
T Consensus         2 ~~gyd~~~t~fsp~Gr~~Qveya~kav~~G~tvigik~~dgVvlaaD~r~~~~~~~-~~~~~ki~~i~~~i~~~~sG~~~   80 (233)
T d1irub_           2 ERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYD-ERSVHKVEPITKHIGLVYSGMGP   80 (233)
T ss_dssp             CCCCCSBSCCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSCEEEEEECCCCCSSBC-STTCCSSEESSSSEEEEEEECHH
T ss_pred             CCCcCCCCCeECCCCcChHHHHHHHHHHcCCCEEEEEeCCEEEEEEeCCcccCCcc-ccccceEEEecCceEEEEeccch
Confidence            68999999999999999999999999999999999999999999999999999875 55789999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceE
Q 025640           82 DANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKA  161 (250)
Q Consensus        82 D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~  161 (250)
                      |++.+.+.++.++..++..++.+++++.+++.++..++.+++....||++++++++|+|+ ++|+||.+||.|++.++++
T Consensus        81 D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~p~~~~~li~g~d~-~~~~ly~id~~G~~~~~~~  159 (233)
T d1irub_          81 DYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGWNE-GRPYLFQSDPSGAYFAWKA  159 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTSBTBCCCSEEEEEEEECS-SSEEEEEECTTSCEEEBSE
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhccccccceEEEeeeeccc-CCceEEEEcCCcceEeccc
Confidence            999999999999999999999999999999999999999999999999999999999998 4899999999999999999


Q ss_pred             EEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHh
Q 025640          162 AAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKH  240 (250)
Q Consensus       162 ~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~  240 (250)
                      +|+|.|+.+++++|++.|+++|+++||++++++||+.+.+++. ++++++|++++++|     +++++++||++++..+
T Consensus       160 ~a~G~gs~~~~~~Le~~~~~~ms~eea~~l~~~~L~~~~~~d~-~~~~vev~ii~~~g-----~~~l~~~eI~~~l~~i  232 (233)
T d1irub_         160 TAMGKNYVNGKTFLEKRYNEDLELEDAIHTAILTLKESFEGQM-TEDNIEVGICNEAG-----FRRLTPTEVKDYLAAI  232 (233)
T ss_dssp             EEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHTTCCSCC-CSSSEEEEEEETTE-----EEECCHHHHHHHHTTC
T ss_pred             eecCCcHHHHHHHHHhhcccCccHHHHHHHHHHHHHHHHhccC-CCCcEEEEEEeCCC-----eEECCHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999998776 66789999999886     8999999999998765

>d1rypa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.4e-60  Score=401.37  Aligned_cols=233  Identities=32%  Similarity=0.520  Sum_probs=219.3

Q ss_pred             CCCCCccccCCCCcccccchHHHHhcCCc-cEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            4 RYDSRTTIFSPEGRLYQVEYAMEAIGNAG-SAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         4 ~yd~~~~~f~p~G~l~qveya~~a~~~g~-t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      +||+++|+|||||||+|||||+||+++|+ |+|||+++||||||+|+|.++++.. .++.+||++|+++++|++||..+|
T Consensus         2 gyd~~~t~fsp~Grl~QvEYA~~av~~~g~T~igik~~dgVvlaad~r~~~~l~~-~~~~~KI~~i~~~i~~~~sG~~~D   80 (243)
T d1rypa_           2 GYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLD-PTTVSYIFCISRTIGMVVNGPIPD   80 (243)
T ss_dssp             GGGGTSSSCCTTSCCHHHHHHHHHTTTTCCCEEEEECSSEEEEEEECCCCCTTBC-GGGCCSEEECSSSCEEEEESCHHH
T ss_pred             CCCCCCCeECCCCeehHHHHHHHHHHccCceEEEEEcCCEEEEEEeccccccccc-cCcccceEecCCCEEEEEecCcHH
Confidence            79999999999999999999999999855 8999999999999999999887655 457789999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+.++.++..|++.++.+++++.+++.+++.++.++++.+.|||++++||+|||+++||+||.+||+|++.+++++
T Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~ls~~~~~~~~~~~~rP~~v~~ll~G~D~~~g~~Ly~~Dp~G~~~~~~~~  160 (243)
T d1rypa_          81 ARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKAT  160 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHBTTSCCCSCEEEEEEEETTTEEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcccccCccceEEEEEEccCCCCeEEEEcCCEEEEecceE
Confidence            99999999999999999999999999999999999999999999999999999999998779999999999999999999


Q ss_pred             EEeCChHHHHHHHHhhCCC-------CCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHH
Q 025640          163 AIGANNQAAQSILKQDYKD-------DISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSK  235 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~~~~-------~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~  235 (250)
                      |+|+|+.+++++|+++|++       +++++||++++++||+.+..++. ++++++|+++++++     +++++++||++
T Consensus       161 a~G~gs~~~~~~Le~~~~~~~~~~~~~~s~eeav~la~~~l~~~~~~d~-~~~~iei~iitk~g-----~~~l~~eeI~~  234 (243)
T d1rypa_         161 ATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEF-SKNDLEVGVATKDK-----FFTLSAENIEE  234 (243)
T ss_dssp             EESTTHHHHHHHHHHHHHHHCSSSCCCSSHHHHHHHHHHHHHHHHTCCC-CTTSEEEEEEETTE-----EEECCHHHHHH
T ss_pred             EeCccHHHHHHHHHHHhhcccccccccccHHHHHHHHHHHHHHHhhccC-CCCcEEEEEEeCCc-----eEEeCHHHHHH
Confidence            9999999999999999974       56999999999999999999874 78899999999986     89999999999


Q ss_pred             HHHHhCCC
Q 025640          236 LLVKHGVT  243 (250)
Q Consensus       236 ~~~~~~~~  243 (250)
                      ++..+.+.
T Consensus       235 ~l~~i~e~  242 (243)
T d1rypa_         235 RLVAIAEQ  242 (243)
T ss_dssp             HHHHHTTT
T ss_pred             HHHHHhcc
Confidence            99987653

>d1rypf_ d.153.1.4 (F:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=8.2e-61  Score=401.74  Aligned_cols=227  Identities=35%  Similarity=0.533  Sum_probs=215.9

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      .+||+++|+|||||||+|||||.||+++|+|+|||+++||||||+|++.++++.   .+.+||+.|+++++|++||..+|
T Consensus         3 ~~yd~~~t~FspdGrl~QvEyA~kav~~g~t~igi~~~dgvvlaad~~~~~~l~---~~~~KI~~I~~~i~~~~sG~~~D   79 (233)
T d1rypf_           3 NNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELS---SYQKKIIKCDEHMGLSLAGLAPD   79 (233)
T ss_dssp             HHHSSCTTCCCTTSCCHHHHHHHHHHHTSCCEEEEECSSEEEEEEECCCSSTTB---CCCCCEEEEETTEEEEEEECHHH
T ss_pred             ccccCCCceECCCCcChHHHHHHHHHHcCCCEEEEEECCeEEEEEeccccccCC---cchheEEEcCCCEEEEEeecccc
Confidence            379999999999999999999999999999999999999999999999998864   35689999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+.++.++..|++.++.+++++.+++.|++.+|.++++.+.|||++++||+|||++ ||+||++||+|++.+++++
T Consensus        80 ~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~l~~~~~~~t~~~~~RP~gv~~il~G~d~~-g~~Ly~idp~G~~~~~~~~  158 (233)
T d1rypf_          80 ARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDKS-GAHLLEFQPSGNVTELYGT  158 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHBTTCCCCCEEEEEEEEETT-EEEEEEECTTSCEEEESEE
T ss_pred             HHHHHHHHHHHHHhhhhhcCCCCcHHHHHHHHHHHHHHHhcccccCCccceEEEEEEcCC-CCEEEEEccccceecccEE
Confidence            999999999999999999999999999999999999999999999999999999999985 8999999999999999999


Q ss_pred             EEeCChHHHHHHHHhh----CCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 025640          163 AIGANNQAAQSILKQD----YKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL  237 (250)
Q Consensus       163 a~G~g~~~~~~~L~~~----~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~  237 (250)
                      |+|.|++.++++|++.    |+++|+++||++++++||+.+.+++..+++.+||++|++++    +|++++++||+.++
T Consensus       159 aiG~gs~~a~~~Le~~~~~~~~~dms~eeai~l~~~~l~~~~~~d~~~~~~iev~ii~k~~----~~~~l~~~ei~~~i  233 (233)
T d1rypf_         159 AIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDT----PFTIYDGEAVAKYI  233 (233)
T ss_dssp             EESTTHHHHHHHHHHHHHHHTTCCSCHHHHHHHHHHHHTTSCCSSCCCTTTEEEEEEETTE----EEEEEEGGGGGGGC
T ss_pred             EecCchHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHHhccCCCCCeEEEEEEECCC----CeEECCHHHHHhhC
Confidence            9999999999999875    47899999999999999999999999999999999999886    59999999998753

>d1rypg_ d.153.1.4 (G:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=7e-60  Score=398.55  Aligned_cols=237  Identities=34%  Similarity=0.555  Sum_probs=222.3

Q ss_pred             CCCCCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHH
Q 025640            3 RRYDSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSD   82 (250)
Q Consensus         3 ~~yd~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D   82 (250)
                      .+||+++|+|||||||+|||||+||+++|+|+|||+++||||||+|++.++++...+ ..+||++|+++++|+++|..+|
T Consensus         2 ~gyd~~~t~fsp~Grl~QvEya~kav~~G~t~igik~~dgVvlaad~~~~~~~~~~~-~~~KI~~I~~~i~~~~sG~~~D   80 (244)
T d1rypg_           2 TGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQ-KNVKIQVVDRHIGCVYSGLIPD   80 (244)
T ss_dssp             CCTTSSTTCCCTTSCCHHHHHHHHHHHTSCCEEEEEETTEEEEEEEEECCCTTBCTT-TSCCCEEETTTEEEEEEECHHH
T ss_pred             CCcCCCCceECCCCeehHHHHHHHHHHcCCCEEEEEeCCEEEEEEecccCCCCcccc-ccceEEEccCceEEEEccchhh
Confidence            589999999999999999999999999999999999999999999999999988765 4689999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEE
Q 025640           83 ANILINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAA  162 (250)
Q Consensus        83 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~  162 (250)
                      ++.+.+.++.++..|++.++.+++++.+++.++..+|.|+++++.|||++++||+|||++ ||+||.+||+|++.+++++
T Consensus        81 ~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~t~~~~~RP~~~~~iiaG~D~~-gp~Ly~idp~Gs~~~~~~~  159 (244)
T d1rypg_          81 GRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKN-GAHLYMLEPSGSYWGYKGA  159 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTSCTTBCCCCEEEEEEEEETT-EEEEEEECTTSCEEEBSEE
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhcccccCCceEEEEEEEEeCC-CCEEEEEcCCccEEecCeE
Confidence            999999999999999999999999999999999999999999999999999999999985 8999999999999999999


Q ss_pred             EEeCChHHHHHHHHh---hCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          163 AIGANNQAAQSILKQ---DYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       163 a~G~g~~~~~~~L~~---~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      |+|.|+..++++||+   .|+++||++||++++++||+.+.+++...+.+++|.+|+.++.. ..++.++.++++.+++.
T Consensus       160 a~G~gs~~~~~~Lek~~~~~~~~mt~eeai~la~~~L~~~~~~~~~~~~~iev~ii~~~~~~-~~~~~~~~e~~~~~~~~  238 (244)
T d1rypg_         160 ATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETN-GLHKFVKGDLLQEAIDF  238 (244)
T ss_dssp             EESTTHHHHHHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHGGGGTTSCEEEEEEEEETTTTT-TSEEECCTHHHHHHHHH
T ss_pred             ecCCccHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHhcccCCCCeEEEEEEEEEcCC-CeEEECCHHHHHHHHHH
Confidence            999999999999996   69999999999999999999999888888889999999865422 24678899999999887


Q ss_pred             hCC
Q 025640          240 HGV  242 (250)
Q Consensus       240 ~~~  242 (250)
                      +++
T Consensus       239 ~~~  241 (244)
T d1rypg_         239 AQK  241 (244)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            764

>d1rype_ d.153.1.4 (E:) Proteasome alpha subunit (non-catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=4.5e-60  Score=399.43  Aligned_cols=236  Identities=38%  Similarity=0.614  Sum_probs=220.3

Q ss_pred             CCCccccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHH
Q 025640            6 DSRTTIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANI   85 (250)
Q Consensus         6 d~~~~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~   85 (250)
                      |+++|+|||||||+|||||+||+++|+|+|||+++||||||+|+|.++++.. .++.+||++|+++++|+++|..+|++.
T Consensus         1 d~~~t~fsp~G~l~Qveya~~a~~~G~t~Vgi~~~dgVvla~d~r~~~~~~~-~~~~~Ki~~i~~~i~~~~sG~~~D~~~   79 (242)
T d1rype_           1 DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE-SDSIEKIVEIDRHIGCAMSGLTADARS   79 (242)
T ss_dssp             CCCTTCBCTTSCBHHHHHHHHHHTTSCCEEEEECSSCEEEEEECCCSSTTBC-GGGCCCEEEEETTEEEEEEESGGGHHH
T ss_pred             CCCcceECCCCcchHHHHHHHHHHcCCCEEEEEeCCEEEEEEeCCccCcCcc-cCccceEEEcCCCEEEEEeecchhHHH
Confidence            8899999999999999999999999999999999999999999999998654 457899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccC------CCcceeEEEEEEEEeCCCCeEEEEECCCCceecc
Q 025640           86 LINTARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFG------GLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW  159 (250)
Q Consensus        86 l~~~~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~------~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~  159 (250)
                      +.++++.++..|++.++.+++++.+++.|++++|.|++..      ++|||+|++||+|||++++|+||++||+|++.++
T Consensus        80 l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~rP~~~~~ii~G~D~~~~p~L~~idp~G~~~~~  159 (242)
T d1rype_          80 MIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRY  159 (242)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHHTTTTCCBSSCTTSCCCBSSCCSEEEEEEEEETTTEEEEEEECTTSCEEEB
T ss_pred             HHHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHhccccccchhccccceEEEEEEEeccccceEEEEEcCCCceecc
Confidence            9999999999999999999999999999999999988764      3799999999999998778999999999999999


Q ss_pred             eEEEEeCChHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHH
Q 025640          160 KAAAIGANNQAAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVK  239 (250)
Q Consensus       160 ~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~  239 (250)
                      +++|+|.|+.+++++|+++|+++||++||++++++||+.+.+++ .+.++++|++|+++.    .++.+++++|++++.+
T Consensus       160 ~~~a~G~gs~~~~~~Le~~~~~~ms~~ea~~la~~~l~~~~~~~-~~~~~~~v~~i~~~~----g~~~l~~~~i~~~~~~  234 (242)
T d1rype_         160 NAKAIGSGSEGAQAELLNEWHSSLTLKEAELLVLKILKQVMEEK-LDENNAQLSCITKQD----GFKIYDNEKTAELIKE  234 (242)
T ss_dssp             SEEEESTTHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHCSSC-CCTTSEEEEEEETTT----EEEECCHHHHHHHHHH
T ss_pred             ceeecccchHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhcc-CCCCceEEEEEECCC----CeEECCHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999866 466689999998764    3899999999999999


Q ss_pred             hCCCCccc
Q 025640          240 HGVTQPAA  247 (250)
Q Consensus       240 ~~~~~~~~  247 (250)
                      +.+...+|
T Consensus       235 i~e~~~~e  242 (242)
T d1rype_         235 LKEKEAAE  242 (242)
T ss_dssp             HHHHHTTC
T ss_pred             HHHhhhcC
Confidence            88765554

>d1yara1 d.153.1.4 (A:13-233) Proteasome alpha subunit (non-catalytic) {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=100.00  E-value=4.1e-59  Score=388.52  Aligned_cols=221  Identities=40%  Similarity=0.706  Sum_probs=209.5

Q ss_pred             cccCCCCcccccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHH
Q 025640           10 TIFSPEGRLYQVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINT   89 (250)
Q Consensus        10 ~~f~p~G~l~qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~   89 (250)
                      |+|||||||+|||||+||+++|+|+|||+++||||||+|+|.+.++.. .++.+||++|+++++|+++|..+|++.+.+.
T Consensus         1 t~fsp~G~l~QvEYa~~av~~G~t~vgi~~~dgVvlaad~r~~~~~~~-~~~~~Ki~~I~~~i~~~~sG~~~D~~~l~~~   79 (221)
T d1yara1           1 TVFSPDGRLFQVEYAREAVKKGSTALGMKFANGVLLISDKKVRSRLIE-QNSIEKIQLIDDYVAAVTSGLVADARVLVDF   79 (221)
T ss_dssp             CCCCTTSCCHHHHHHHHHHTTSCCEEEEEETTEEEEEECCCCCCTTBC-STTCCSEEEEETTEEEEEEEBHHHHHHHHHH
T ss_pred             CeECCCCcchHHHHHHHHHhcCCcEEEEEeCCEEEEEEecccCCcccc-cCccceEEEecCCceEEeeeccchHHHHHHH
Confidence            799999999999999999999999999999999999999998866554 5678999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChH
Q 025640           90 ARVQAQRYTYAYQEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQ  169 (250)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~  169 (250)
                      ++.++..|++.++++++++.+++.++..++.++++.+.|||++++||||||++ ||+||++||.|++.+++++|+|+|+.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~l~~~~a~~~~~~~~~~~~rP~~~~~li~G~d~~-gp~Ly~id~~G~~~~~~~~a~G~g~~  158 (221)
T d1yara1          80 ARISAQQEKVTYGSLVNIENLVKRVADQMQQYTQYGGVRPYGVSLIFAGIDQI-GPRLFDCDPAGTINEYKATAIGSGKD  158 (221)
T ss_dssp             HHHHHHHHHHHHSSCCCHHHHHHHHHHHHHHTTTBTTBCCCCEEEEEEEECSS-CEEEEEECTTCCEEEBSEEEESTTHH
T ss_pred             HHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhhhccCCCcceEEEEEEEecC-CCeEEEEcCCccEEEeeEEEECCchH
Confidence            99999999999999999999999999999999999999999999999999985 89999999999999999999999999


Q ss_pred             HHHHHHHhhCCCCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 025640          170 AAQSILKQDYKDDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL  237 (250)
Q Consensus       170 ~~~~~L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~  237 (250)
                      .++++|++.|+++||++||++++++||+.+.++ ..+.++++|++|++++    .+|+++++||+.+|
T Consensus       159 ~~~~~Le~~~~~~ms~~ea~~la~~~l~~~~~~-~~~~~~~ei~~i~~~~----~~r~l~~~ei~~~l  221 (221)
T d1yara1         159 AVVSFLEREYKENLPEKEAVTLGIKALKSSLEE-GEELKAPEIASITVGN----KYRIYDQEEVKKFL  221 (221)
T ss_dssp             HHHHHHHHHCCTTCCHHHHHHHHHHHHHHTSCS-SCCCCCCEEEEEETTS----CCEECCHHHHHTTC
T ss_pred             HHHHHHHHHhhccccHHHHHHHHHHHHHHHHhc-cCCCCCcEEEEEEcCC----CEEECCHHHHHHhC
Confidence            999999999999999999999999999999875 4677899999999876    48999999998764

>d1q5qa_ d.153.1.4 (A:) Proteasome alpha subunit (non-catalytic) {Rhodococcus erythropolis [TaxId: 1833]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome alpha subunit (non-catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

Probab=100.00  E-value=1.3e-46  Score=313.67  Aligned_cols=209  Identities=20%  Similarity=0.263  Sum_probs=182.6

Q ss_pred             ccchHHHHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHH
Q 025640           20 QVEYAMEAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTY   99 (250)
Q Consensus        20 qveya~~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~   99 (250)
                      |+|||.||+++|+|+|||+++||||||+|+|.+        +.+||++|++||+||++|..+|++.+.+.++.++..|++
T Consensus         8 q~eyA~~av~~GtT~vgi~~~~GVvlaad~r~~--------s~~KI~~i~~~i~~~~sG~~aD~~~l~~~~r~~~~~~~~   79 (227)
T d1q5qa_           8 RSELARKGIARGRSVVVLTFRDGVLFVAENPST--------ALHKVSELYDRLGFAAVGKYNEFENLRRAGIVHADMRGY   79 (227)
T ss_dssp             HHHHHHHHHHTSCCEEEEECSSEEEEEECCSCS--------SSCSEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCEEEEEECCEEEEEEccCCC--------CcceEEEecCceEEEecCchHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999843        468999999999999999999999999999999999999


Q ss_pred             HhCC-CCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCC---CCeEEEEECCCCceecce-EEEEeCChHHHHHH
Q 025640          100 AYQE-PMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKN---YGFQLYMSDPSGNYGGWK-AAAIGANNQAAQSI  174 (250)
Q Consensus       100 ~~~~-~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~---~~~~Ly~vd~~G~~~~~~-~~a~G~g~~~~~~~  174 (250)
                      .++. +++++.+++.+++.++.. +..+.|||+|++||||||..   .+|+||.+||+|++.+++ +++.|.++++++++
T Consensus        80 ~~~~~~~~~~~la~~~~~~~~~~-~~~~~rP~gvs~lvaG~D~~g~~~~p~Ly~vDpsG~~~~~~~~~~~g~~s~~~~~~  158 (227)
T d1q5qa_          80 SYDRRDVTGRSLANAYAQTLGTI-FTEQPKPYEVEICVAEVGRVGSPKAPQLYRITYDGSIVDEQHFVVMGGTTEPIATA  158 (227)
T ss_dssp             HSCGGGCCHHHHHHHHHHHHHHH-HHHSSSCCCEEEEEEECCCSSCCCCCEEEEEETTSCEEEESSEEEESSSHHHHHHH
T ss_pred             HhCCCCCcHHHHHHHHHHHHHHH-HHhcCCCceEEEEEEEEecCCCCCCCEEEEEccccceeeecccccCCCchHHHHHH
Confidence            9985 689999999999876543 33367999999999999863   479999999999988766 45666778899999


Q ss_pred             HHhhCCCCCCHHHHHHHHHHHHHHhhcCCC----CCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHH
Q 025640          175 LKQDYKDDISREEAVQLALKVLSKTMDSTS----LTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLV  238 (250)
Q Consensus       175 L~~~~~~~~s~~ea~~l~~~~l~~~~~~~~----~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~  238 (250)
                      |+++|+++||++||++++++||+.+..++.    ..+.+++|+++++++.+ ..|++++++||+++++
T Consensus       159 Le~~y~~~ms~eea~~la~~aL~~a~~~d~~~~~~~~~~ievavi~k~~~~-~~fr~l~~~ei~~~l~  225 (227)
T d1q5qa_         159 MRESYRADLDLEAAVGIAVNALRQGGAGEGEKRNVDVASLEVAVLDQSRPR-RAFRRIAGTALEQLVP  225 (227)
T ss_dssp             HHHHCCTTCCHHHHHHHHHHHHTTCC--------CCSSCSEEEEEETTSSS-CCEEECCHHHHHTTSC
T ss_pred             HHHhccCCCCHHHHHHHHHHHHHHHhhcccccCCcCcceEEEEEEECCCCc-cceEEcCHHHHHHHhc
Confidence            999999999999999999999999987653    46778999999988732 3699999999998764

>d1yarh1 d.153.1.4 (H:1-203) Proteasome beta subunit (catalytic) {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=100.00  E-value=1.2e-45  Score=302.97  Aligned_cols=200  Identities=21%  Similarity=0.373  Sum_probs=190.5

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      ||+|||+++||||||+|+|.+.|.++.+++.+|||+|+++++||++|..+|++.+.+.++.+++.+++.++.+++++.++
T Consensus         1 TT~igi~~kdgVvia~D~r~s~~~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (203)
T d1yarh1           1 TTTVGITLKDAVIMATERRVTMENFIMHKNGKKLFQIDTYTGMTIAGLVGDAQVLVRYMKAELELYRLQRRVNMPIEAVA   80 (203)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CcEEEEEECCEEEEEECCCcccCCEeecCCcccEEEecCCeeeecCCCcchHHHHHHHHHHHHHHHHHhcCCCCcHHHHH
Confidence            68999999999999999999999888888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.++++++.++    .||+++++|+||+|+  +|+||.+||+|++.+++++|+|+|+++++++|++.|+++||++||+++
T Consensus        81 ~~l~~~~~~~~----~~p~~~~~lvaG~d~--~p~l~~~d~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~eea~~l  154 (203)
T d1yarh1          81 TLLSNMLNQVK----YMPYMVQLLVGGIDT--APHVFSIDAAGGSVEDIYASTGSGSPFVYGVLESQYSEKMTVDEGVDL  154 (203)
T ss_dssp             HHHHHHHHHTT----TSCCCEEEEEEEESS--SEEEEEECTTCCEEEESEEEESTTHHHHHHHHHHHCCTTCCHHHHHHH
T ss_pred             HHHHHHHHhhc----cCCccceeEEEEEcC--CCeeEecCCccceecccccccCCCcHHHHHHHHHhccCCCCHHHHHHH
Confidence            99999888663    589999999999986  599999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHG  241 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~  241 (250)
                      +++||+.+.+++..++++++|++|+++.    .++.++++||+.++.++.
T Consensus       155 ~~~~l~~~~~~d~~~~~~v~v~ii~~~~----g~~~l~~~ei~~~~~~~~  200 (203)
T d1yarh1         155 VIRAISAAKQRDSASGGMIDVAVITRKD----GYVQLPTDQIESRIRKLG  200 (203)
T ss_dssp             HHHHHHHHHHHCTTCCSCCEEEEEETTT----EEEECCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhcCCCCCeEEEEEEECCC----CEEECCHHHHHHHHHHhC
Confidence            9999999999999999999999999764    389999999999999875

>d1ryph_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=4e-46  Score=306.34  Aligned_cols=200  Identities=17%  Similarity=0.294  Sum_probs=187.2

Q ss_pred             HhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCC
Q 025640           27 AIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMP  106 (250)
Q Consensus        27 a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~  106 (250)
                      .+++|+|+|||+++||||||+|+|.+++.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++.. +
T Consensus         5 ~v~~GtTivgi~~~dgVvlaaD~r~s~g~~i~~~~~~ki~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~-~   83 (205)
T d1ryph_           5 EVSLGASIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGTP-S   83 (205)
T ss_dssp             CCBCCCCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEEBHHHHHHHHHHHHHHHHHHHHHHSSC-C
T ss_pred             cccCcceEEEEEECCEEEEEECCccccCceeeccccceEEEccCceEEeeccchhHHHHHHHHHHHHHHHHHHHcCCc-c
Confidence            478999999999999999999999999999988899999999999999999999999999999999999999999865 5


Q ss_pred             HHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHH
Q 025640          107 VEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISRE  186 (250)
Q Consensus       107 ~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~  186 (250)
                      +..+++.++++++.+     .+|+++++||||||+.++|+||.+||.|++.+++++|+|+|+.+++++|++.|+++||++
T Consensus        84 ~~~~~~~~~~~~~~~-----~~p~~~~~lvaG~d~~~~p~Ly~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~ms~~  158 (205)
T d1ryph_          84 TETAASVFKELCYEN-----KDNLTAGIIVAGYDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKE  158 (205)
T ss_dssp             HHHHHHHHHHHHHHT-----TTTCCEEEEEEEEETTTEEEEEEECTTSCCEEESEEEESGGGGGGHHHHHHHCCTTCCHH
T ss_pred             HHHHHHHHHHHHHhC-----ccCceEEEEEEeecCCCCcEEEEECCCCcEEecCeEEeecCcHHHHHHHHhhhhcccCHH
Confidence            788899999888654     379999999999998779999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHH
Q 025640          187 EAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSK  235 (250)
Q Consensus       187 ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~  235 (250)
                      ||++++++||+.+.+||..++++++|++|+++|   ..++.+.++||++
T Consensus       159 ea~~l~~~al~~a~~rD~~sg~~v~v~iitk~G---~~~~~~~~~e~~~  204 (205)
T d1ryph_         159 ETVDFIKHSLSQAIKWDGSSGGVIRMVVLTAAG---VERLIFYPDEYEQ  204 (205)
T ss_dssp             HHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTE---EEEEEECHHHHTC
T ss_pred             HHHHHHHHHHHHHHHhcCcCCCCEEEEEEcCCc---eEEEecCcccccc
Confidence            999999999999999999999999999999987   4556789999864

>d1irul_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=4.8e-46  Score=304.94  Aligned_cols=200  Identities=19%  Similarity=0.278  Sum_probs=191.3

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      ||+|||+++||||||+|+|.++|.++.+++.+|||+|+++++|+++|..+|++.+.+.++.++..|++.++.+++++.++
T Consensus         1 TT~igi~~~dgVvlaaD~~~t~g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (201)
T d1irul_           1 TTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAAS   80 (201)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEEcCccccCCEeecCCcccEEEeCCcEEEEEcCccchHHHHHHHHHHHHHHHHHhcCCCCchhHHH
Confidence            68999999999999999999999998888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.+|.++    .+|++++++++|+|+. +|+||.+||+|++.+++++|+|+|+.+++++|++.|+++||.+||+++
T Consensus        81 ~~l~~~~~~~~----~~p~~~~~lvaG~d~~-~~~l~~~d~~G~~~~~~~~a~G~g~~~~~~~Le~~~~~~ms~eea~~l  155 (201)
T d1irul_          81 KLLANMVYQYK----GMGLSMGTMICGWDKR-GPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDL  155 (201)
T ss_dssp             HHHHHHHHTTT----TSCCCBEEEEEEECSS-SEEEEEEESSSCEEECSEEEESTTHHHHHHHHHTTCCTTCCHHHHHHH
T ss_pred             HHHHHHhhhcc----CCCceEEEEEEEEecC-CceEEEEccCceEEEeeeEEecCchHHHHHHHHhhccCCCCHHHHHHH
Confidence            99999998764    4799999999999985 899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHG  241 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~  241 (250)
                      +++||+.+.++|..++++++|++|+++|     +++++++||.++..++.
T Consensus       156 ~~~~l~~~~~~d~~sg~~~~v~~i~~~G-----~~~i~~~ev~~~~~~~~  200 (201)
T d1irul_         156 ARRAIYQATYRDAYSGGAVNLYHVREDG-----WIRVSSDNVADLHEKYS  200 (201)
T ss_dssp             HHHHHHHHHHHBTTCCSEEEEEEECSSC-----EEEEEEEEHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCCCCceEEEEEeCCc-----eEEECHHHHHHHHHhhc
Confidence            9999999999999999999999999998     78899999999987753

>d1j2qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=100.00  E-value=2.4e-45  Score=300.69  Aligned_cols=201  Identities=26%  Similarity=0.430  Sum_probs=191.2

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      ||+|||+++||||||+|+|.+.|.++.+++.+|||+|+++++||++|..+|++.+.+.++.++..|++.++.+++++.++
T Consensus         1 TT~vgi~~~dgVvlaaD~r~s~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (202)
T d1j2qh_           1 TTTVGLVCKDGVVMATEKRATMGNFIASKAAKKIYQIADRMAMTTAGSVGDAQFLARIIKIEANLYEIRRERKPTVRAIA   80 (202)
T ss_dssp             CCEEEEEETTEEEEEEECCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CcEEEEEECCEEEEEECCCcccCCeeccCccceEEEecCcEEEEecCcchhHHHHHHHHHHHhhhhhhccCCCccHHHHH
Confidence            68999999999999999999999888888899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecc-eEEEEeCChHHHHHHHHhhCCCCCCHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGW-KAAAIGANNQAAQSILKQDYKDDISREEAVQ  190 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~-~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~  190 (250)
                      +.+++++|.+++    +|+++++|+||+|+. +|+||.+||+|++.++ +++|+|+|+.+++++|++.|+++||++||++
T Consensus        81 ~~~~~~~~~~~~----~p~~~~~lvaG~d~~-~~~l~~~d~~G~~~~~~~~~a~G~g~~~~~~~Le~~~~~~ms~~ea~~  155 (202)
T d1j2qh_          81 TLTSNLLNSYRY----FPYLVQLLIGGIDSE-GKSIYSIDPIGGAIEEKDIVATGSGSLTAYGVLEDRFTPEIGVDEAVE  155 (202)
T ss_dssp             HHHHHHHHHTTT----SCCCEEEEEEEEETT-EEEEEEECTTCCEEEESSEEEESTTHHHHHHHHHHHCCTTCCHHHHHH
T ss_pred             HHHHHHHhhhcc----cceeeEEEEEEEcCC-CceEEEEeCCCCeEeecceEEccCChHHHHHHHHhhcCCCCCHHHHHH
Confidence            999999998753    799999999999985 8999999999998765 5999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhCC
Q 025640          191 LALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGV  242 (250)
Q Consensus       191 l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~  242 (250)
                      ++++||+.+.+++..++++++|++|+++|     +++++++||++++.++++
T Consensus       156 l~~~al~~~~~~d~~~g~~v~v~~i~~~g-----~~~~~~~ei~~~l~~~~k  202 (202)
T d1j2qh_         156 LAVRAIYSAMKRDSASGDGIDVVKITEDE-----FYQYSPEEVEQILAKFRK  202 (202)
T ss_dssp             HHHHHHHHHHTTCTTSCSCEEEEEECSSC-----EEECHHHHHHHHGGGTTC
T ss_pred             HHHHHHHHHHHhcCCCCCeEEEEEEECCC-----EEEeCHHHHHHHHHHhhC
Confidence            99999999999999999999999999987     899999999999998865

>d1rypk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=4e-46  Score=304.75  Aligned_cols=195  Identities=19%  Similarity=0.209  Sum_probs=185.8

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +|+|||+++||||||+|+|.+.|.++.+++.+||++|++|++|+++|..+|++.+.+.++.++..|++.++.+++++.++
T Consensus         2 ~tiigi~~~dgVvlaaD~r~s~g~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   81 (198)
T d1rypk_           2 DIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVS   81 (198)
T ss_dssp             CCEEEEECSSCEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             eEEEEEEECCEEEEEEcCCcccCCEeecCccceEEEecCCEEEEecCCcccHHHHHHHHHHHHHHHHHHhCCCcchHHHH
Confidence            68999999999999999999999999888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCC-CCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKN-YGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQ  190 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~-~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~  190 (250)
                      +.++..++.+++  ..|||++++||||||+. ++|+||.+||.|++.+++++++|.|+.+++++|+++|+++|+++||++
T Consensus        82 ~~i~~~~~~~~~--~~~P~~~~~liaG~D~~~~~p~L~~id~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~~~~eea~~  159 (198)
T d1rypk_          82 SFVRQELAKSIR--SRRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLD  159 (198)
T ss_dssp             HHHHHHHHHHTT--SSSCCCEEEEEEEEETTTTEEEEEEECTTCCEEECSEEECTTHHHHHHHHHHHHCCTTCCHHHHHH
T ss_pred             HHHHHHHHHHHh--cccccceEEEEEEEecCCCceEEEEecccccEEecceEEEeccchhhHHHHHhcccccCCHHHHHH
Confidence            999999987665  47999999999999974 589999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHH
Q 025640          191 LALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEAL  233 (250)
Q Consensus       191 l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei  233 (250)
                      ++++||+.+.+|+..++++++|++|+++|     +++++++++
T Consensus       160 l~~~~l~~~~~~d~~s~~~~~v~vi~~dG-----~~~~~~~~~  197 (198)
T d1rypk_         160 LLKLCVQELEKRMPMDFKGVIVKIVDKDG-----IRQVDDFQA  197 (198)
T ss_dssp             HHHHHHHHHHHHCSBCCCCEEEEEEETTE-----EEEECCCSC
T ss_pred             HHHHHHHHHHHhcCcCCCcEEEEEEcCCC-----eEEcchhcc
Confidence            99999999999999999999999999997     788888765

>d1rypl_ d.153.1.4 (L:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.5e-45  Score=304.48  Aligned_cols=202  Identities=15%  Similarity=0.208  Sum_probs=192.5

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      ||+|||+++||||||+|+|.++|.++.+++.+|||+|+++++|+++|..+|++.+.+.++.++..|++.++.+++++.++
T Consensus         1 TT~iai~~kdgVvlaaD~r~t~g~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (212)
T d1rypl_           1 TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAAS   80 (212)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEEETTEEEECCBCHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEEcCccccCceeecCCcceEEEECCcEEEEeccchHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHH
Confidence            68999999999999999999999988888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++++|.++    ..|+++..+++|++++.+|+||.+||+|++.+++++|+|+|+.+++++|++.|+++||++||+++
T Consensus        81 ~~ls~~~~~~~----~~p~~~~~~l~G~~~~~g~~Ly~id~~G~~~~~~~~a~G~gs~~~~~~Le~~~~~~mt~~ea~~l  156 (212)
T d1rypl_          81 KILSNLVYQYK----GAGLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYL  156 (212)
T ss_dssp             HHHHHHHHHTT----TSCCCBEEEEEEEETTTEEEEEEEETTCCEEECSEEEESTTHHHHHHHHHHHCCTTCCHHHHHHH
T ss_pred             HHHHHHHHHhc----cCCcceEeeeeEeecCCCCEEEEECCCceEEecceEEEccCcccchhHHHHhccCCCCHHHHHHH
Confidence            99999998763    46899999999999888999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHHHHhCC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLLVKHGV  242 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~  242 (250)
                      +++||+.+.+||..++++++|++|+++|     +++++++||.+++.++++
T Consensus       157 ~~~al~~~~~rd~~sg~~v~v~vi~~~g-----~~~~~~~ev~~~~~~~~~  202 (212)
T d1rypl_         157 GKRSILAAAHRDAYSGGSVNLYHVTEDG-----WIYHGNHDVGELFWKVKE  202 (212)
T ss_dssp             HHHHHHHHHHHBTTCCSEEEEEEEETTE-----EEEEEEEEHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCCceEEEEEcCCc-----eEEeCHHHHHHHHHHHHH
Confidence            9999999999999999999999999997     899999999998877664

>d1iruh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=7e-45  Score=298.21  Aligned_cols=198  Identities=20%  Similarity=0.286  Sum_probs=187.8

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      ||+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..|++.++.+++++.++
T Consensus         1 TTivai~~~dgVvlaaD~r~t~g~~i~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (202)
T d1iruh_           1 TTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAA   80 (202)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEECCccccCCeeecCCcceEEEcCCcEEEEeccchHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            68999999999999999999999999988999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      ++++..++.++     +|+++++|++|||+.++|+||.+||.|++.+.+++|+|+|+.+++++|++.|+++|+++||+++
T Consensus        81 ~~l~~~l~~~~-----~p~~~~~lvaG~d~~~~~~l~~~d~~g~~~~~~~~a~G~g~~~a~~~L~~~~~~~~~~~ea~~l  155 (202)
T d1iruh_          81 SLFKEMCYRYR-----EDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQF  155 (202)
T ss_dssp             HHHHHHHHHTT-----TTCCEEEEEEEEETTTEEEEEEECTTSCCEECSEEEESGGGGGGHHHHHHHCCTTCCHHHHHHH
T ss_pred             HHHHHHHHhhc-----cceeEEEEEEEeecCCCcEEEEECCCCceeecceeEEeCCHHHHHHHHHHhhccCCcHHHHHHH
Confidence            99999988753     6999999999999888999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHHHH
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSKLL  237 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~~~  237 (250)
                      +++||+.+.+||..++++++|++|+++|   ..++.++++||+.++
T Consensus       156 ~~~al~~a~~rD~~sg~~i~v~vi~~~G---~~~~~~~~d~~~~~~  198 (202)
T d1iruh_         156 TANALALAMERDGSSGGVIRLAAIAESG---VERQVLLGDQIPKFA  198 (202)
T ss_dssp             HHHHHHHHHHHBTTCCSCEEEEEEETTE---EEEEEECGGGSCCCC
T ss_pred             HHHHHHHHHhhCCCCCCCEEEEEEeCCC---eEEEEcCHHHhhhhh
Confidence            9999999999999999999999999987   456779999876543

>d1irui_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=1.6e-43  Score=293.66  Aligned_cols=193  Identities=18%  Similarity=0.276  Sum_probs=182.8

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      ||+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..+++.++..++++.++
T Consensus         1 TTivgi~~~dgVvlaaD~r~s~g~~i~~~~~~KI~~i~~~i~~~~aG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a   80 (220)
T d1irui_           1 TTIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTAN   80 (220)
T ss_dssp             CCEEEEEETTEEEEEECCCEESSSBEEESSCCCEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHCSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEEcCCcccCCEeecCCcccEEEecCcEEEEEccccHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHH
Confidence            68999999999999999999999999988999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.++.+     .+|+++++|++|+|++ ||+||.+||.|++.+++++|+|+|+.+++++|++.|+++||++||+++
T Consensus        81 ~~l~~~~y~~-----~~p~~~~~ivaG~D~~-g~~L~~id~~G~~~~~~~~a~Gsgs~~a~~~L~~~~~~~~s~~ea~~l  154 (220)
T d1irui_          81 RMLKQMLFRY-----RGYIGAALVLGGVDVT-GPHLYSIYPHGSTDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNL  154 (220)
T ss_dssp             HHHHHHHHHT-----TTCSCEEEEEEEECSS-CEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHSCCTTCCHHHHHTH
T ss_pred             HHHHhhhhhc-----ccccceeEEEEEEeCC-CcEEEEEeCCCcEEEeeEEEEccccHHHHHHHHHhcccCCCHHHHHHH
Confidence            9999998754     4799999999999985 899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHH
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSK  235 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~  235 (250)
                      +++||+.+.++|+.++++|+|++|+++|     ++.+.+.+++.
T Consensus       155 ~~~al~~~~~~D~~sg~~i~i~vitkdg-----~~~~~~~~~~~  193 (220)
T d1irui_         155 VSEAIAAGIFNDLGSGSNIDLCVISKNK-----LDFLRPYTVPN  193 (220)
T ss_dssp             HHHHHHHHHHHCTTCCSCEEEEEEETTE-----EECCSEEECCC
T ss_pred             HHHHHHHhhccCCCCCCcEEEEEEECCC-----eEEeCcccccc
Confidence            9999999999999999999999999997     67777766544

>d1ryp2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=7.4e-44  Score=298.18  Aligned_cols=204  Identities=14%  Similarity=0.137  Sum_probs=188.7

Q ss_pred             HHhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHh----
Q 025640           26 EAIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAY----  101 (250)
Q Consensus        26 ~a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~----  101 (250)
                      +++..|+|+|||+++||||||+|+|.+.|.+..+++.+||++|+++++|+++|..+|++.+.+.++.++..+++.+    
T Consensus         3 ~~i~tGtTivgi~~~dgVvlaaD~r~s~g~~~~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~   82 (233)
T d1ryp2_           3 QPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLAD   82 (233)
T ss_dssp             CCCEEECCEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHTTCTTTT
T ss_pred             CCccccceEEEEEECCEEEEEECCCcccCCeeecCCcceEEEeCCCEEEEeccCchHHHHHHHHHHHHHHHHHHhhCCCC
Confidence            5778999999999999999999999998888878889999999999999999999999999999999999998776    


Q ss_pred             -CCCCCHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCC
Q 025640          102 -QEPMPVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK  180 (250)
Q Consensus       102 -~~~~~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~  180 (250)
                       +..++++.+++++++.++  +++.++||+++++||+|||++++|+||.+||.|++.+++++|+|+|+++++++|++.|+
T Consensus        83 ~~~~~~~~~~a~~l~~~~y--~~~~~~~P~~~~~liaG~d~~g~~~ly~~d~~G~~~~~~~~a~G~g~~~a~~~Le~~~~  160 (233)
T d1ryp2_          83 AEEALEPSYIFEYLATVMY--QRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVD  160 (233)
T ss_dssp             TTTSCCHHHHHHHHHHHHH--HHHHTTCCCCEEEEEEEECTTSCEEEEEEETTCCEECCSEEECTHHHHHHHHHHTTTCC
T ss_pred             CCcccCHHHHHHHHHHHHH--hhccccCCceeEEEEEEEcCCCCeEEEEEcCCCcEEeeeeEEecCccHHHHHHHHHHHh
Confidence             567899999999998774  45557899999999999999888999999999999999999999999999999999998


Q ss_pred             -----CCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHH
Q 025640          181 -----DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSK  235 (250)
Q Consensus       181 -----~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~  235 (250)
                           |+|+++||++++++||+.+.+||+.++++|+|++|++|+    .++.+.+++|+.
T Consensus       161 ~~~~~~~ms~eeA~~l~~~al~~~~~rD~~sg~~i~i~~itkd~----g~~~~~~~~ie~  216 (233)
T d1ryp2_         161 RESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNT----GLTFKKNLQVEN  216 (233)
T ss_dssp             SGGGGGGCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTT----EEEEEEEEECCS
T ss_pred             hcccccccCHHHHHHHHHHHHHHHHHhcccCCCCEEEEEEECCC----CEEECChhcchh
Confidence                 789999999999999999999999999999999999985    378888888765

>d1iruj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=8.8e-42  Score=280.05  Aligned_cols=189  Identities=11%  Similarity=0.139  Sum_probs=178.4

Q ss_pred             HhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCC
Q 025640           27 AIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMP  106 (250)
Q Consensus        27 a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~  106 (250)
                      ...||+|+|||+++||||||+|+|.+.|.++.+++.+||++|+++++||++|..+|++.+.+.++.++..|++.++.+++
T Consensus         3 ~~~nG~Tvigi~~~dgVvlaaD~r~s~g~~~~~~~~~Ki~~I~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~   82 (204)
T d1iruj_           3 MSYNGGAVMAMKGKNCVAIAADRRFGIQAQLVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFRLNLYELKEGRQIK   82 (204)
T ss_dssp             TTSSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEECSTTEEEECCSCHHHHHHHHHHHHHHHHHHHHHSSSCCC
T ss_pred             eeeCCceEEEEEECCEEEEEECCCcccCCeeEcCcccEEEEeCCCeEEEeccCchHHHHHHHHHHHhhhhhhhhcccccc
Confidence            35689999999999999999999999999998889999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCC-CeEEEEECCCCceec-ceEEEEeCChHHHHHHHHhhCCCCCC
Q 025640          107 VEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNY-GFQLYMSDPSGNYGG-WKAAAIGANNQAAQSILKQDYKDDIS  184 (250)
Q Consensus       107 ~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~-~~~Ly~vd~~G~~~~-~~~~a~G~g~~~~~~~L~~~~~~~~s  184 (250)
                      ++.+++.++..+|.++    .+|+++++||||||+++ +|.+|.+||.|.... ..++++|+|+++++++|++.|+++|+
T Consensus        83 ~~~~a~~l~~~~~~~~----~~p~~~~~lvaG~D~~~~~~~~~~~d~~g~~~~~~~~~~~G~g~~~~~~~l~~~~~~~ms  158 (204)
T d1iruj_          83 PYTLMSMVANLLYEKR----FGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMD  158 (204)
T ss_dssp             HHHHHHHHHHHHHTTT----TSCCSCCCEEEEECTTSCCEEEEEECTTCCEEECSSEEEEETTHHHHHHHHHHHCCSSCC
T ss_pred             hHHHHHHHHHHHHHhh----hccceeEEEEEEEcCCCCceEEEEecCCCceeeecceEEechhHHHHHHHHHhccccCCC
Confidence            9999999999988653    57999999999999754 689999999998665 56899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          185 REEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       185 ~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      ++||++++++||+.+.+||..++++++|++|+++|
T Consensus       159 ~~ea~~l~~~al~~a~~rd~~sg~~~~v~ii~k~g  193 (204)
T d1iruj_         159 PDHLFETISQAMLNAVDRDAVSGMGVIVHIIEKDK  193 (204)
T ss_dssp             HHHHHHHHHHHHHHHGGGBTTSCSCEEEEEEESSB
T ss_pred             HHHHHHHHHHHHHHHHhhcccCCCcEEEEEEeCCC
Confidence            99999999999999999999999999999999997

>d1ryp1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=8.7e-42  Score=283.43  Aligned_cols=188  Identities=20%  Similarity=0.307  Sum_probs=175.8

Q ss_pred             hcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhC-CCCC
Q 025640           28 IGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQ-EPMP  106 (250)
Q Consensus        28 ~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~-~~~~  106 (250)
                      +.||+|+|||+++||||||+|+|.+.+.++.+++.+||++|+++++++++|..+|++.+.+.++.++..|++.++ ..++
T Consensus         6 ~~nG~Tivgi~~~dgVviaaD~r~s~~~~i~~~~~~KI~~I~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~   85 (222)
T d1ryp1_           6 GDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLS   85 (222)
T ss_dssp             CCCCCEEEEEECSSCEEEEEECCEEETTEEEESCCCCCEECSTTCEEEEEESHHHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             cCCCcEEEEEEECCEEEEEECCCcccCCEeccCCcceEEEecCCEEEEeccChHHHHHHHHHHHHHhhhhhhhcCCCCCc
Confidence            379999999999999999999999999998888899999999999999999999999999999999999998876 4678


Q ss_pred             HHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCC------
Q 025640          107 VEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK------  180 (250)
Q Consensus       107 ~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~------  180 (250)
                      +..+++.++..++.    .+.||+++++||+|+|++++|+||.+||+|++.+++++|+|+|+++++++||+.|+      
T Consensus        86 ~~~~~~~~~~~~~~----~~~~p~~~~~li~G~d~~~~~~Ly~~D~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~~~  161 (222)
T d1ryp1_          86 INSAARNIQHLLYG----KRFFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYE  161 (222)
T ss_dssp             HHHHHHHHHHHHHT----TTTSCCCEEEEEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTSCTTCBC
T ss_pred             HHHHHHHHHHHHHh----hhhhhheeeeeEEEEeCCCCeEEEEECCCcEEEEeceEEEcccHHHHHHHHHHhhccccccC
Confidence            88888887776654    35799999999999999878999999999999999999999999999999999887      


Q ss_pred             -----------CCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          181 -----------DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       181 -----------~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                                 ++||++||++++.+||+.+.+||+.++++++|++|++||
T Consensus       162 ~~~~~~~~~~~~~lt~~ea~~l~~~al~~a~~rd~~sg~~v~v~iitkdG  211 (222)
T d1ryp1_         162 PGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDG  211 (222)
T ss_dssp             TTSTTCSBCCCCCCCHHHHHHHHHHHHHHHHHHBTTCCSEEEEEEEETTE
T ss_pred             cccchhhhcccccccHHHHHHHHHHHHHHHHHhcccCCCcEEEEEEeCCC
Confidence                       689999999999999999999999999999999999997

>d1rypj_ d.153.1.4 (J:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.9e-41  Score=276.78  Aligned_cols=187  Identities=17%  Similarity=0.178  Sum_probs=176.4

Q ss_pred             hcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCH
Q 025640           28 IGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPV  107 (250)
Q Consensus        28 ~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~  107 (250)
                      ..||+|+|||+++||||||+|+|.+++.++.+++.+||+++ ++++++++|..+|++.+.+.++.++..|++.++.++++
T Consensus         5 ~~nG~Tivgi~~~d~VvlaaD~r~~~~~~~~~~~~~Ki~~i-~~i~~~~~G~~~D~~~l~~~~~~~~~~~~~~~~~~~~~   83 (204)
T d1rypj_           5 SINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHY-GHVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEP   83 (204)
T ss_dssp             GSSCCEEEEEECSSEEEEEEECCEEETTEEEESCCCCEEEE-TTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCH
T ss_pred             ccCCeEEEEEEECCEEEEEEcCCcccCCEeecCcccEEEEc-CCEEEEecCcchHHHHHHHHHHHHHHHHHHhcCCCCcc
Confidence            46899999999999999999999999999888889999999 59999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCC-CeEEEEECCCCceecc-eEEEEeCChHHHHHHHHhhCCCCCCH
Q 025640          108 EQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNY-GFQLYMSDPSGNYGGW-KAAAIGANNQAAQSILKQDYKDDISR  185 (250)
Q Consensus       108 ~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~-~~~Ly~vd~~G~~~~~-~~~a~G~g~~~~~~~L~~~~~~~~s~  185 (250)
                      +.+++.+++.+|.++    .+|+++++|++|||+.. .|+||++||+|++.++ .++++|.|+.+++++|++.|+++|++
T Consensus        84 ~~la~~l~~~l~~~~----~~p~~v~~li~G~d~~~g~~~L~~~D~~G~~~~~~~~~~~G~g~~~a~~~l~~~~~~~ms~  159 (204)
T d1rypj_          84 ETFTQLVSSSLYERR----FGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEP  159 (204)
T ss_dssp             HHHHHHHHHHHHTTT----TSCCCEEEEEEEECTTTCCEEEEEECTTCCEECCSSEEEEETTHHHHHHHHHHHCCSSCCH
T ss_pred             hHHHHHHHHHHHhhc----ccceeeeEEEEEEecCCCcceEEEeCCCCccccccCcEEeecchHHHHHHHHhccccCCCH
Confidence            999999999988653    48999999999999654 4899999999999876 48888999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          186 EEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       186 ~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                      +||++++++||..+.+++..++++++|++|+++|
T Consensus       160 ~ea~~l~~~al~~a~~~d~~sg~~~~v~ii~kdg  193 (204)
T d1rypj_         160 EDLFETISQALLNAADRDALSGWGAVVYIIKKDE  193 (204)
T ss_dssp             HHHHHHHHHHHHHHHTTBTTSCSCEEEEEEESSC
T ss_pred             HHHHHHHHHHHHHHHHhcCccCCeEEEEEEECCc
Confidence            9999999999999999999999999999999997

>d1rypi_ d.153.1.4 (I:) Proteasome beta subunit (catalytic) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.2e-41  Score=282.72  Aligned_cols=183  Identities=19%  Similarity=0.271  Sum_probs=174.9

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      ||+|||+++||||||+|+|.+.|.++.+++.+||++|+++++||++|..+|++.+.+.++.++..+++.++.++++..++
T Consensus         1 TTiVgik~~dGVviaaD~r~s~g~~~~~~~~~KI~~I~~~i~~~~sG~~aD~~~l~~~l~~~~~~~~~~~~~~~~v~~~a   80 (222)
T d1rypi_           1 TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSAL   80 (222)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESSCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCceeecCCcccEEEEcCCEEEEecccchHHHHHHHHHHHHHHHhhhhhCCCCcHHHHH
Confidence            68999999999999999999999998888899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.+++.++.+     .+|+++++|+||+|+ .||+||.+||.|++.+++++|+|+|+++++++|++.|+++||++||+++
T Consensus        81 ~~l~~~~~~~-----~~p~~~~~l~aG~d~-~g~~Ly~id~~G~~~~~~~~a~Gsg~~~a~~~Le~~~k~~ms~eea~~l  154 (222)
T d1rypi_          81 QMLKQHLFKY-----QGHIGAYLIVAGVDP-TGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKL  154 (222)
T ss_dssp             HHHHHHHHHT-----TTCSCEEEEEEEEET-TEEEEEEECTTSCEEECSEEEESTTHHHHHHHHHHHCCSSCCHHHHHHH
T ss_pred             HHHHHHHHhh-----hhccceeEEEEEEcC-CCcEEEEEecCcceEEeeEEEECCCcHHHHHHHHhhccCCCCHHHHHHH
Confidence            9999887653     479999999999998 5999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCC
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPS  220 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~  220 (250)
                      +++||+.+.+||..++++++|+++++++.
T Consensus       155 ~~~al~~a~~~D~~sg~~i~i~vi~~~~~  183 (222)
T d1rypi_         155 ASDAIQAGIWNDLGSGSNVDVCVMEIGKD  183 (222)
T ss_dssp             HHHHHHHHHHHCTTCCSCEEEEEEETTSC
T ss_pred             HHHHHHHHhcccCCCCCcEEEEEEEcCCC
Confidence            99999999999999999999999998763

>d1q5qh_ d.153.1.4 (H:) Proteasome beta subunit (catalytic) {Rhodococcus erythropolis [TaxId: 1833]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Rhodococcus erythropolis [TaxId: 1833]

Probab=100.00  E-value=8.7e-42  Score=283.67  Aligned_cols=209  Identities=22%  Similarity=0.257  Sum_probs=191.4

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      ||+|||+++||||||+|+|.++|.++.+++.+||++|+++++|+++|..+|++.+.+.++.++..+++.++.++++..++
T Consensus         1 TTivgi~~kdgVvlaaD~r~s~g~~i~~~~~~KI~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   80 (224)
T d1q5qh_           1 TTIVALTYKGGVLLAGDRRATQGNLIASRDVEKVYVTDEYSAAGIAGTAGIAIELVRLFAVELEHYEKIEGVPLTFDGKA   80 (224)
T ss_dssp             CCEEEEECSSCEEEEECCCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCCEeecCCcceEEEeCCcEEEEecccchHHHHHHHHHHHHhHHHHHhhCCCccHHHHH
Confidence            68999999999999999999999888888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEe-----CCCCeEEEEECCCCceecc--eEEEEeCChHHHHHHHHhhCCCCCC
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWD-----KNYGFQLYMSDPSGNYGGW--KAAAIGANNQAAQSILKQDYKDDIS  184 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d-----~~~~~~Ly~vd~~G~~~~~--~~~a~G~g~~~~~~~L~~~~~~~~s  184 (250)
                      +.+++.++.+++ ...+|+++.++++|++     +..+|+||.+||+|++.++  +++|+|+|+.+++++|++.|+++||
T Consensus        81 ~~~~~~~~~~~~-~~~~~~~~~~~~~g~~~~g~d~~~~~~l~~~d~~G~~~~~~~~~~a~GsG~~~a~~~Le~~~~~~mt  159 (224)
T d1q5qh_          81 NRLASMVRGNLG-AAMQGLAVVPLLVGYDLDADDESRAGRIVSYDVVGGRYEERAGYHAVGSGSLFAKSALKKIYSPDSD  159 (224)
T ss_dssp             HHHHHHHHTTHH-HHTTTCCEEEEEEEECTTCSSTTSCEEEEEECTTSCEEECCSSEEEESTTHHHHHHHHHHHCCTTCC
T ss_pred             HHHHHHHHHhhc-ccccCccceeeEEEeecccccccCCceEEEEEccCcEEEeccceeeecCccHHHHHHHHHhhcccCC
Confidence            999999998865 3567778877777765     4558999999999998654  7899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCCCc-------EEEEEEEeCCCCceeEEECCHHHHHHHHHHhCCCCcc
Q 025640          185 REEAVQLALKVLSKTMDSTSLTSDK-------LELAEVFLMPSGKVKYQVCSPEALSKLLVKHGVTQPA  246 (250)
Q Consensus       185 ~~ea~~l~~~~l~~~~~~~~~~~~~-------iei~ii~~~~~~~~~~~~~~~~ei~~~~~~~~~~~~~  246 (250)
                      ++||++++++||+.+.+||..+|+.       +++++++++|     +++++++|+++++.++.+.|.+
T Consensus       160 ~~ea~~l~~~al~~a~~rD~~SGg~~~~~~~~~~~~~i~~~g-----~~~l~~~ei~~~~~~~~~~~~~  223 (224)
T d1q5qh_         160 EETALRAAIESLYDAADDDSATGGPDLTRGIYPTAVTITQAG-----AVHVSEETTSELARRIVAERTE  223 (224)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCCBTTTTBCCEEEEEETTE-----EEECCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhhccccCCcccccccceEEEEEeCCc-----EEEcCHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999988874       8899999998     8999999999999988765543

>d1iru2_ d.153.1.4 (2:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=1.1e-42  Score=288.16  Aligned_cols=201  Identities=13%  Similarity=0.115  Sum_probs=183.8

Q ss_pred             HhcCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHH-hCCCC
Q 025640           27 AIGNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYA-YQEPM  105 (250)
Q Consensus        27 a~~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~-~~~~~  105 (250)
                      ++.+|+|+|||+++||||||+|+|.+.|.++.+++.+||++|+++++||++|..+|++.+.+.++.++..+... ++.++
T Consensus         4 ~~~~GtTivgi~~~dgVviaaD~r~t~g~~~~~~~~~KI~~i~~~i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~~~   83 (217)
T d1iru2_           4 PMVTGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEELLGDGHSY   83 (217)
T ss_dssp             CCSEECCCEEEEETTEEEEEEECCEEETTEEEECSCCCEEEETTTEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCSSCCC
T ss_pred             CcCcccEEEEEEECCEEEEEEcCCcccCCeeecCCcceEEEeCCCeEEEeccccHHHHHHHHHHHHHHHHhhhhcCCCCC
Confidence            46789999999999999999999999998888889999999999999999999999999999999988887754 56899


Q ss_pred             CHHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhC--CCCC
Q 025640          106 PVEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDY--KDDI  183 (250)
Q Consensus       106 ~~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~--~~~~  183 (250)
                      +++.+++.+++.++  +++...+|+++++|++|+|+ ++|+||.+||+|++.+++++|+|+|+.+++++|++.|  +++|
T Consensus        84 ~v~~~a~~l~~~~y--~~~~~~~p~~~~~li~G~d~-~~~~l~~~D~~G~~~~~~~~a~G~g~~~a~~~Le~~~~~~~~l  160 (217)
T d1iru2_          84 SPRAIHSWLTRAMY--SRRSKMNPLWNTMVIGGYAD-GESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVL  160 (217)
T ss_dssp             CHHHHHHHHHHHHH--HHHHTTCCCCEEEEEEEEET-TEEEEEEECSSCCEEECSEEECTTHHHHTHHHHHHHHTSCSCC
T ss_pred             CHHHHHHHHHHHHH--HhccccCcccceEEEEEEcC-CCcEEEEEecCceeEeeeEEeccCcHHHHHHHHHHHhcccCCC
Confidence            99999999998774  55567899999999999997 5899999999999999999999999999999999965  4899


Q ss_pred             CHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHHHHHH
Q 025640          184 SREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPEALSK  235 (250)
Q Consensus       184 s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~ei~~  235 (250)
                      |.+||++++++||+.+.+||..++++++|++|+++|     ++...+++++.
T Consensus       161 t~~ea~~l~~~al~~a~~rd~~sg~~i~i~vi~~~G-----~~~~~~~~~~~  207 (217)
T d1iru2_         161 SQTEARDLVERCMRVLYYRDARSYNRFQTATVTEKG-----VEIEGPLSTET  207 (217)
T ss_dssp             CHHHHHHHHHHHHHHHHHHBTTCCSCEEEEEEETTE-----EEEEEEECCCC
T ss_pred             CHHHHHHHHHHHHHHHHHhcCcCCCcEEEEEEeCCC-----EEEcCCeeccc
Confidence            999999999999999999999999999999999997     56666665543

>d1iru1_ d.153.1.4 (1:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=8.6e-40  Score=269.01  Aligned_cols=187  Identities=19%  Similarity=0.257  Sum_probs=179.1

Q ss_pred             cCCccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHH
Q 025640           29 GNAGSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVE  108 (250)
Q Consensus        29 ~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~  108 (250)
                      .||+|+|||+++||||||+|+|.+.|.++.+++.+||++|+++++++++|..+|++.+.++++.++..+++.++.++++.
T Consensus         7 ~nG~Tivai~~~dgVviaaD~r~t~g~~~~~~~~~KI~~i~~~i~~~~aG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~   86 (213)
T d1iru1_           7 FNGGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTG   86 (213)
T ss_dssp             CCCCEEEEEEETTEEEEEEECCEEETTEEEESCCCCEEEEETTEEEEEEECHHHHHHHHHHHHHHHHHHHHHHSSCCCHH
T ss_pred             CCCcEEEEEEECCEEEEEECCccccCceeeccccCEEEEcCCCEEEEecCccchHHHHHHHHHHHHHHHHHhhCCchhHH
Confidence            68999999999999999999999999888888899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCC--------
Q 025640          109 QLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK--------  180 (250)
Q Consensus       109 ~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~--------  180 (250)
                      .+++.++..++.++    .+|++++.+++|||..++|.+|.+||.|++.+++++++|+|+.+++++|++.|.        
T Consensus        87 ~~~~~~~~~~~~~~----~~~~~~~~~~~g~d~~~~~~l~~~d~~g~~~~~~~~a~G~g~~~a~~~l~~~~~~~~~~~~~  162 (213)
T d1iru1_          87 AIAAMLSTILYSRR----FFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVE  162 (213)
T ss_dssp             HHHHHHHHHHHTTT----TSCCCEEEEEEEECTTSCEEEEEECTTSCEEEESEEEEETTHHHHHHHHHHHTTCCSCSSCC
T ss_pred             HHHHHHHHHHHHHH----hhhcccccceEEEecCCCcEEEecCCcceeeecCeeeecCccHHHHHHHHHhhcccchhccc
Confidence            99999999998764    579999999999999888999999999999999999999999999999998764        


Q ss_pred             -CCCCHHHHHHHHHHHHHHhhcCCCCCCCcEEEEEEEeCC
Q 025640          181 -DDISREEAVQLALKVLSKTMDSTSLTSDKLELAEVFLMP  219 (250)
Q Consensus       181 -~~~s~~ea~~l~~~~l~~~~~~~~~~~~~iei~ii~~~~  219 (250)
                       ++||++||++++++||..+.+++..++++++|++|+++|
T Consensus       163 ~~~~s~~ea~~~~~~~l~~~~~~d~~sg~~~~v~~i~k~G  202 (213)
T d1iru1_         163 HVPLSLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEG  202 (213)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHHHBTTSCSEEEEEEEETTE
T ss_pred             ccCCCHHHHHHHHHHHHHHHHHhcCCCCCceEEEEEeCCC
Confidence             789999999999999999999999999999999999998

>d1iruk_ d.153.1.4 (K:) Proteasome beta subunit (catalytic) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: Proteasome beta subunit (catalytic)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=4.1e-40  Score=267.44  Aligned_cols=193  Identities=21%  Similarity=0.229  Sum_probs=182.8

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      +++|||+++||||||+|+|.+.|.+..+++.+||++|+++++++++|..+|++.+.+.++.++..|...++.+++++.++
T Consensus         2 t~ivgi~~kdgVviaaD~r~~~g~~~~~~~~~Ki~~i~~~i~~~~~G~~aD~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   81 (199)
T d1iruk_           2 EYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGYELSPTAAA   81 (199)
T ss_dssp             CCEEEEECSSEEEEEEECCEEETTEEEESSCCCEEECSSSEEEEEEESTTHHHHHHHHHHHHHHHHHHHHSSCCCHHHHH
T ss_pred             eEEEEEEECCEEEEEECCCccCCCeeecCCcceEEEecCcEEEEecccchHHHHHHHHHHHHhhhhhhhcCCcCcHHHHH
Confidence            68999999999999999999999998888889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQL  191 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~l  191 (250)
                      +.++..++.+.+  ..+|++++++++|||+..+|+||.+||.|.+.+.+++++|+|+.+++++|++.|+++|+++||+++
T Consensus        82 ~~l~~~~~~~~~--~~~~~~~~~~~aG~d~~~~~~l~~~~~~g~~~~~~~~a~G~gs~~a~~~l~~~~~~~~~~~ea~~l  159 (199)
T d1iruk_          82 NFTRRNLADCLR--SRTPYHVNLLLAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVEL  159 (199)
T ss_dssp             HHHHHHHHHHHT--SSSCCCEEEEEEEEETTTEEEEEEECTTCCEEECSEEEESHHHHHHHHHHHHHCCTTCCHHHHHHH
T ss_pred             HHHHHHHHHHhh--ccCCcceeeeecceeccCCceEEeecccceEEeeeeeeecccchhhhHHHHHhccCCCCHHHHHHH
Confidence            999988876543  578999999999999988899999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCCCCCCcEEEEEEEeCCCCceeEEECCHH
Q 025640          192 ALKVLSKTMDSTSLTSDKLELAEVFLMPSGKVKYQVCSPE  231 (250)
Q Consensus       192 ~~~~l~~~~~~~~~~~~~iei~ii~~~~~~~~~~~~~~~~  231 (250)
                      +++||+.+.++|..++++++|++|+++|     ++.+++.
T Consensus       160 ~~~al~~~~~~d~~sg~~~~v~vv~~~g-----~~~~~~~  194 (199)
T d1iruk_         160 LRKCLEELQKRFILNLPTFSVRIIDKNG-----IHDLDNI  194 (199)
T ss_dssp             HHHHHHHHHHTBCBCCCCEEEEEEETTE-----EECCCCB
T ss_pred             HHHHHHHHHHhcCCcCCceEEEEEcCCC-----eEEcCCc
Confidence            9999999999999999999999999998     6766653

>d2z3ba1 d.153.1.4 (A:1-180) HslV (ClpQ) protease {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: HslV (ClpQ) protease
species: Bacillus subtilis [TaxId: 1423]

Probab=99.93  E-value=7.6e-26  Score=180.80  Aligned_cols=175  Identities=17%  Similarity=0.054  Sum_probs=129.2

Q ss_pred             cCCccEEEEEeCCEEEEEEEcccCCCcccccC-CcCcEEEecCc-eEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCC
Q 025640           29 GNAGSAIGILSKDGVVLVGEKKVTSKLLQTST-STEKMYKIDDH-VACAVAGIMSDANILINTARVQAQRYTYAYQEPMP  106 (250)
Q Consensus        29 ~~g~t~igi~~~dgvvla~d~~~~~~~~~~~~-~~~Ki~~i~~~-i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~  106 (250)
                      -+|+|+|||+++||||||+|+|+++|.++..+ ..+|++.++++ ++++.+|..+|.+.+.+..+.+...+.     ...
T Consensus         3 ~~GTTivai~~~dGVvlAaDtR~S~G~~i~~~~~~~ki~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~-----~~~   77 (180)
T d2z3ba1           3 FHATTIFAVQHKGRSAMSGDGQVTFGQAVVMKHTARKVRKLFNGKVLAGFAGSVADAFTLFEKFEAKLEEYN-----GNL   77 (180)
T ss_dssp             BCCCCEEEEEETTEEEEEECCCEEETTTEEEESCCCCEEEETTTTEEEEECSCHHHHHHHHHHHHHHHHHTT-----TCH
T ss_pred             CCCeEEEEEEECCEEEEEECCcccCCceeEecccceEEEEecccceecccchHHHHHHHHHHHHHHHHHhhc-----ccc
Confidence            47999999999999999999999998765554 57899999775 777889999999988877765554332     111


Q ss_pred             HHHHHHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHH
Q 025640          107 VEQLVQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISRE  186 (250)
Q Consensus       107 ~~~la~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~  186 (250)
                      ...+.............+....++.+....+|++.. ++.++..+      ..++.++|+|+.+++++|++.|+++|+.+
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~------~~~~~a~GSGs~~A~g~l~~~~~~~~s~~  150 (180)
T d2z3ba1          78 KRAAVELAKEWRSDKVLRKLEAMLIVMNQDTLLLVS-GTGEVIEP------DDGILAIGSGGNYALAAGRALKKHAGESM  150 (180)
T ss_dssp             HHHHHHHHHHHHHCTTGGGCCCCEEEECSSCEEEEC-TTCCEECC------SSSEEEESTTHHHHHHHHHHHHHHHGGGC
T ss_pred             chhHHHHHHHHhHHHHHHHhhcceeeeecccccccc-CCceeecc------cccEEEEcCchHHHHHHHHHHhhcCCCcc
Confidence            222222222222222222234445444444455442 44444444      44588999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          187 EAVQLALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       187 ea~~l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      ||++++++||+.+.++|.+++++++|.+|
T Consensus       151 eA~~l~~~Al~~A~e~dvyT~~~~~~~~i  179 (180)
T d2z3ba1         151 SASEIARAALETAGEICVYTNDQIILEEL  179 (180)
T ss_dssp             CHHHHHHHHHHHHHHHCTTCCSCCEEEEE
T ss_pred             CHHHHHHHHHHHHHhhcEEcCCcEEEEEe
Confidence            99999999999999999999999999887

>d1m4ya_ d.153.1.4 (A:) HslV (ClpQ) protease {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: HslV (ClpQ) protease
species: Thermotoga maritima [TaxId: 2336]

Probab=99.91  E-value=3.4e-25  Score=175.38  Aligned_cols=170  Identities=15%  Similarity=0.042  Sum_probs=132.0

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEEEEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVACAVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQLV  111 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la  111 (250)
                      ||+|||+++||||||+|+|.+.|.++.+++.+|+++|+++++++.+|..+|.+.+..........+.  .+   ......
T Consensus         1 TTivav~~~~gVviAaDtR~S~G~~i~~r~~~Ki~~i~~~~~~~~~g~~ad~~~~~~~~~~~~~~~~--~~---~~~~~~   75 (171)
T d1m4ya_           1 TTILVVRRNGQTVMGGDGQVTFGSTVLKGNARKVRKLGEGKVLAGFAGSVADAMTLFDRFEAKLREW--GG---NLTKAA   75 (171)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHHHT--TT---CHHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCCEEEeCCcceEEEecCCcEEEEEeechhhHHHHHHHHHHHHHHh--hc---cchhhH
Confidence            6899999999999999999999999999999999999999999999999999887776655444322  11   122222


Q ss_pred             HHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCC-CCCCHHHHHH
Q 025640          112 QSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYK-DDISREEAVQ  190 (250)
Q Consensus       112 ~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~-~~~s~~ea~~  190 (250)
                      ...+..+....     .++....++.+.++ .+|+++..|+.|.....++.|+|+|+.+++++|+..++ ++++   |.+
T Consensus        76 ~~~~~~~~~~~-----~~~~~~~~~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~l~~~~~~~~~~---a~e  146 (171)
T d1m4ya_          76 VELAKDWRTDR-----VLRRLEALLLVADK-ENIFIISGNGEVIQPDDDAAAIGSGGPYALAAAKALLRNTDLS---ARE  146 (171)
T ss_dssp             HHHHHHHHHCT-----TGGGCCCEEEEECS-SCEEEECTTSCEECCSSSEEEESTTHHHHHHHHHHHHHHCCCC---HHH
T ss_pred             HHHHHHHHHhh-----hhcccccccceecC-CcceEEecCCceeeecCCEEEEcchHHHHHHHHHhhccCCCCC---HHH
Confidence            22222221111     12222334444555 58999999999999999999999999999999998765 5775   778


Q ss_pred             HHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          191 LALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       191 l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      ++++||+.+.++|.+++++++|..|
T Consensus       147 l~~~Ai~~A~e~dvyTg~~~~i~~~  171 (171)
T d1m4ya_         147 IVEKAMTIAGEICIYTNQNIVIEEV  171 (171)
T ss_dssp             HHHHHHHHHHHHCTTCCSCCEEEEC
T ss_pred             HHHHHHHHHHhhceEcCCcEEEEEC
Confidence            9999999999999999999998653

>d1g3ka_ d.153.1.4 (A:) HslV (ClpQ) protease {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: Ntn hydrolase-like
superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases)
family: Proteasome subunits
domain: HslV (ClpQ) protease
species: Haemophilus influenzae [TaxId: 727]

Probab=99.91  E-value=5.4e-24  Score=168.72  Aligned_cols=171  Identities=13%  Similarity=0.044  Sum_probs=126.5

Q ss_pred             ccEEEEEeCCEEEEEEEcccCCCcccccCCcCcEEEecCceEE-EEeCchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Q 025640           32 GSAIGILSKDGVVLVGEKKVTSKLLQTSTSTEKMYKIDDHVAC-AVAGIMSDANILINTARVQAQRYTYAYQEPMPVEQL  110 (250)
Q Consensus        32 ~t~igi~~~dgvvla~d~~~~~~~~~~~~~~~Ki~~i~~~i~~-~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l  110 (250)
                      ||+|||+++||||||+|+|++.|.++.+++.+||++|++++++ +.+|...+.+.+.+..+....     .. .......
T Consensus         1 TTivai~~~dGVVlAaDtRaS~G~~i~~r~~~Ki~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~-~~~~~~~   74 (173)
T d1g3ka_           1 TTIVSVRRNGQVVVGGDGQVSLGNTVMKGNARKVRRLYNGKVLAGFAGGTADAFTLFELFERKLE-----MH-QGHLLKS   74 (173)
T ss_dssp             CCEEEEEETTEEEEEECCCEEETTEEEESCCCCEEEETTTTEEEEEESCHHHHHHHHHHHHHHHH-----HT-TTCHHHH
T ss_pred             CeEEEEEECCEEEEEECCCcccCCEeEcCCcceEEEecCCcEEEEeeehhHhHHHHHHHHHHHHH-----hh-cCcchhH
Confidence            6899999999999999999999999999999999999887555 555555555544433322221     11 2223333


Q ss_pred             HHHHHHHHhhccccCCCcceeEEEEEEEEeCCCCeEEEEECCCCceecceEEEEeCChHHHHHHHHhhCCCCCCHHHHHH
Q 025640          111 VQSLCDTKQGYTQFGGLRPFGVSFLFAGWDKNYGFQLYMSDPSGNYGGWKAAAIGANNQAAQSILKQDYKDDISREEAVQ  190 (250)
Q Consensus       111 a~~l~~~~~~~~~~~~~rP~~~~~iv~G~d~~~~~~Ly~vd~~G~~~~~~~~a~G~g~~~~~~~L~~~~~~~~s~~ea~~  190 (250)
                      +..++..+....    ..+..... +.|++..+++.++..|+.|++.+.++.|+|+|+.++.+.|+.+++  ++.+||.+
T Consensus        75 ~~~~~~~~~~~~----~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~a~GSGs~~A~~~l~~~~~--~~~~~A~e  147 (173)
T d1g3ka_          75 AVELAKDWRTDR----ALRKLEAM-LIVADEKESLIITGIGDVVQPEEDQILAIGSGGNYALSAARALVE--NTELSAHE  147 (173)
T ss_dssp             HHHHHHHHHHST----TGGGCCCE-EEEECSSCEEEEETTTEEECCCTTCEEEESTTHHHHHHHHHHHHH--HCCCCHHH
T ss_pred             HHHHHHHHHHhh----hhcccccc-cccccCCCcceecccCceEEecCCCEEEecchHHHHHHHHHHhhh--cCCCCHHH
Confidence            333333332221    22233333 345556678999999999999999999999999999999998875  34456899


Q ss_pred             HHHHHHHHhhcCCCCCCCcEEEEEE
Q 025640          191 LALKVLSKTMDSTSLTSDKLELAEV  215 (250)
Q Consensus       191 l~~~~l~~~~~~~~~~~~~iei~ii  215 (250)
                      ++++||+.+.++|.+++++++|..|
T Consensus       148 la~~Ai~~Aae~dvyTgd~~~i~~~  172 (173)
T d1g3ka_         148 IVEKSLRIAGDICVFTNTNFTIEEL  172 (173)
T ss_dssp             HHHHHHHHHHHHCTTCCSCCEEEEE
T ss_pred             HHHHHHHHHHhhcEEcCCcEEEEEC
Confidence            9999999999999999999999876